BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716722.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,013,179 number of mapped reads = 922,092 (91.01%) number of supplementary alignments = 5,454 (0.54%) number of secondary alignments = 0 number of mapped bases = 54,057,539 bp number of sequenced bases = 54,043,219 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,379 duplication rate = 1.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6391 >>>>>>> ACTG content number of A's = 13,530,379 bp (25.04%) number of C's = 10,392,989 bp (19.23%) number of T's = 17,059,842 bp (31.57%) number of G's = 13,059,259 bp (24.16%) number of N's = 750 bp (0%) GC percentage = 43.4% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 258,060 number of insertions = 3,719 mapped reads with insertion percentage = 0.4% number of deletions = 9,241 mapped reads with deletion percentage = 1% homopolymer indels = 42.72% >>>>>>> Coverage mean coverageData = 0.0175X std coverageData = 0.1893X There is a 1.62% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4071487 0.016334912160559874 0.22800611379677327 chr2 243199373 5013765 0.020615863183167007 0.2092457405435213 chr3 198022430 4117016 0.020790654876823803 0.15814794443193136 chr4 191154276 3065867 0.016038704778960845 0.14023644489462475 chr5 180915260 2759486 0.015252920068765895 0.13004276735721734 chr6 171115067 3054953 0.01785320868325406 0.14634810646298246 chr7 159138663 3432031 0.021566292787064574 0.40504789192596646 chr8 146364022 4361081 0.029796127083744666 0.2218828556738372 chr9 141213431 2322807 0.016448909877418105 0.1488936536446073 chr10 135534747 2618757 0.019321665166792984 0.2418817386506514 chr11 135006516 1844753 0.013664177512735756 0.13869671106846407 chr12 133851895 2589068 0.01934278181119513 0.1576269182780642 chr13 115169878 1092415 0.009485249259359292 0.10179593976249775 chr14 107349540 1372584 0.012786119064879085 0.12094556237404638 chr15 102531392 1326303 0.012935579768584435 0.12066787058793993 chr16 90354753 1669550 0.01847772191906717 0.1475287225089956 chr17 81195210 2305900 0.028399458539487735 0.18380740465143394 chr18 78077248 1250384 0.016014703796937105 0.20525783070246698 chr19 59128983 1093123 0.018487092869498532 0.22999527226209435 chr20 63025520 1217639 0.01931977713154925 0.15020452720448443 chr21 48129895 559228 0.011619140245371406 0.11837081407214423 chr22 51304566 806323 0.01571639841958706 0.13204138799806137 chrMT 16571 63610 3.8386337577695975 2.869133337493189 chrX 155270560 1929184 0.01242466054092933 0.12831946869053237 chrY 59373566 120225 0.0020248910095782354 0.061901012602786507