Needleman paramter effect on SNV/Indel ratio,,,,
"We use the default Needlman paramters everywhere in our analyses which is, gap opening penalty set to the maximum (10) with low gap extenstion penatly (set to 0.5) ",,,,
We test here the SNV/Indel ratio when lowering the gap opening penalty to 0.5 and increasing the gap extention to 10,,,,
Sample,SNV frequency default parameters,Indel frequency  default parameters,SNV frequency low gap opening penalty high gap extention penalty,Indel frequency low gap opening penalty high gap extention penalty
JAX_HiFi_NA19317_m64119_220501_151001,0.07,0.93,0.05,0.95
JAX_HiFi_HG03371_m64039_220209_170329,0.06,0.94,0.03,0.97
JAX_HiFi_NA19650_m64119_211228_031859,0.04,0.96,0.02,0.98
JAX_HiFi_HG04217_m64119_210213_082612,0.05,0.95,0.03,0.97
JAX_HiFi_NA19317_m64119_210702_094450,0.07,0.93,0.04,0.96
JAX_HiFi_HG02106_m64039_210117_062206,0.04,0.96,0.02,0.98
JAX_HiFi_HG01457_m64119_210701_004527,0.05,0.95,0.03,0.97
JAX_HiFi_HG01596_m64119_220214_210708,0.05,0.95,0.03,0.97
JAX_HiFi_NA19347_m64039_210620_163340,0.05,0.95,0.02,0.98
JAX_HiFi_NA19384_m64119_211223_194521,0.06,0.94,0.03,0.97
JAX_HiFi_HG02106_m64119_210122_231012,0.04,0.96,0.02,0.98
JAX_HiFi_HG03807_m64119_210124_053806,0.05,0.95,0.04,0.96
GM18989_20210510_Lee_m64119_210501_214725.ccs,0.06,0.94,0.03,0.97
JAX_HiFi_NA19331_m64119_210503_041604,0.05,0.95,0.03,0.97
JAX_HiFi_HG02666_m64119_210708_195851,0.04,0.96,0.02,0.98
JAX_HiFi_HG01890_m64039_211213_024848,0.06,0.94,0.04,0.96
JAX_HiFi_HG00096_m64119_220224_171953,0.04,0.96,0.02,0.98
JAX_HiFi_NA20509_m64119_220204_203221,0.05,0.95,0.03,0.97
JAX_HiFi_NA18989_m64039_210616_161955,0.04,0.96,0.02,0.98
JAX_HiFi_HG02492_m64039_220221_051108,0.06,0.94,0.03,0.97
JAX_HiFi_HG01457_m64119_211210_191732,0.05,0.95,0.03,0.97
JAX_HiFi_HG02106_m64119_210210_174344,0.03,0.97,0.02,0.98
JAX_HiFi_HG01890_m64039_211124_052608,0.05,0.95,0.04,0.96
JAX_HiFi_HG01596_m64119_220209_052029,0.05,0.95,0.03,0.97
JAX_HiFi_HG03456_m64039_220111_082237,0.06,0.94,0.04,0.96
JAX_HiFi_HG01457_m64119_210723_055657,0.05,0.95,0.03,0.97
GM18989_20210513_Lee_m64039_210508_014218.ccs,0.07,0.93,0.03,0.97
JAX_HiFi_HG02492_m64119_220206_072658,0.07,0.93,0.04,0.96
JAX_HiFi_NA19705_m64039_220109_212617,0.06,0.94,0.04,0.96
JAX_HiFi_NA19331_m64039_210510_142933,0.06,0.94,0.02,0.98
JAX_HiFi_HG03456_m64119_211226_162136,0.04,0.96,0.02,0.98
JAX_HiFi_HG00268_m64039_210116_000705,0.04,0.96,0.02,0.98
JAX_HiFi_NA19384_m64039_211219_103338,0.07,0.93,0.04,0.96
JAX_HiFi_NA18534_m64119_220117_195935,0.04,0.96,0.02,0.98
JAX_HiFi_HG00096_m64039_220218_071556,0.05,0.95,0.03,0.97
JAX_HiFi_NA19317_m64039_210601_195743,0.06,0.94,0.03,0.97
JAX_HiFi_HG00268_m64119_210113_164007,0.05,0.95,0.02,0.98
JAX_HiFi_NA18989_m64119_211008_181054,0.05,0.95,0.02,0.98
JAX_HiFi_HG02011_m64119_220104_202343,0.06,0.94,0.04,0.96
JAX_HiFi_HG04217_m64119_210212_015818,0.04,0.96,0.03,0.97
GM19331_20210510_Lee_m64119_210503_041604.ccs,0.05,0.95,0.03,0.97
JAX_HiFi_HG03009_m64119_220119_065557,0.05,0.95,0.03,0.97
JAX_HiFi_HG02011_m64039_220121_204950,0.05,0.95,0.03,0.97
JAX_HiFi_NA19384_m64119_210621_120219,0.05,0.95,0.02,0.98
JAX_HiFi_HG00358_m64119_211213_170947,0.06,0.94,0.03,0.97
JAX_HiFi_HG03807_m64119_210125_120547,0.05,0.95,0.03,0.97
JAX_HiFi_HG01457_m64039_211217_233816,0.04,0.96,0.02,0.98
JAX_HiFi_NA18534_m64119_220124_155829,0.04,0.96,0.02,0.98
JAX_HiFi_HG00268_m64119_210121_165545,0.05,0.95,0.02,0.98
JAX_HiFi_HG01505_m64119_220302_072750,0.05,0.95,0.03,0.97
JAX_HiFi_NA18989_m64039_211119_203548,0.06,0.94,0.05,0.95
GM19331_20210513_Lee_m64039_210510_142933.ccs,0.06,0.94,0.02,0.98
JAX_HiFi_HG02011_m64119_220114_220850,0.06,0.94,0.04,0.96
JAX_HiFi_NA19317_m64039_210607_200243,0.06,0.94,0.03,0.97
JAX_HiFi_NA19347_m64119_220509_164847,0.05,0.95,0.02,0.98
JAX_HiFi_NA19347_m64119_220503_020657,0.06,0.94,0.03,0.97
JAX_HiFi_HG03248_m64039_210628_130740,0.04,0.96,0.03,0.97
JAX_HiFi_NA20509_m64119_220211_173309,0.05,0.95,0.03,0.97
JAX_HiFi_NA20509_m64039_220219_181334,0.05,0.95,0.03,0.97
JAX_HiFi_HG03248_m64119_210613_003658,0.03,0.97,0.02,0.98
JAX_HiFi_HG03248_m64119_210613_003658,0.03,0.97,0.03,0.97
GM18989_20210513_Lee_m64039_210506_192609.ccs,0.06,0.94,0.03,0.97
GM18989_20210513_Lee_m64039_210506_192609.ccs,0.06,0.94,0.06,0.94
JAX_HiFi_HG03065_m64119_220121_210303,0.06,0.94,0.04,0.96
JAX_HiFi_NA19317_m64119_220521_031347,0.06,0.94,0.05,0.95
JAX_HiFi_HG00358_m64039_211211_155133,0.05,0.95,0.03,0.97
JAX_HiFi_HG03248_m64039_210710_005846,0.04,0.96,0.02,0.98
JAX_HiFi_NA19317_m64119_220506_185510,0.07,0.93,0.04,0.96
JAX_HiFi_HG00096_m64039_220211_040031,0.05,0.95,0.04,0.96
JAX_HiFi_HG03065_m64119_220116_090326,0.06,0.94,0.04,0.96
JAX_HiFi_HG03807_m64039_210118_125023,0.05,0.95,0.02,0.98
JAX_HiFi_NA19705_m64119_220106_071815,0.07,0.93,0.06,0.94
,,,,
,,0.9479166667,,0.9695833333