BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717065.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 = 1,180,355 number of mapped reads = 1,071,505 (90.78%) number of supplementary alignments = 5,710 (0.48%) number of secondary alignments = 0 number of mapped bases = 62,556,925 bp number of sequenced bases = 62,538,878 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,619 duplication rate = 1.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4822 >>>>>>> ACTG content number of A's = 16,063,725 bp (25.69%) number of C's = 11,545,027 bp (18.46%) number of T's = 19,264,966 bp (30.8%) number of G's = 15,664,412 bp (25.05%) number of N's = 748 bp (0%) GC percentage = 43.51% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 305,193 number of insertions = 5,078 mapped reads with insertion percentage = 0.47% number of deletions = 11,533 mapped reads with deletion percentage = 1.07% homopolymer indels = 39.09% >>>>>>> Coverage mean coverageData = 0.0202X std coverageData = 0.2049X There is a 1.87% of reference with a coverageData >= 1X There is a 0.11% 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 5279473 0.02118138353605145 0.2864295120974501 chr2 243199373 6322513 0.0259972421886137 0.2457855640161991 chr3 198022430 4567580 0.023065972879940923 0.16529023916313948 chr4 191154276 3570267 0.018677411118964454 0.15220050393936552 chr5 180915260 3190210 0.017633725314271445 0.14044316012669122 chr6 171115067 3573024 0.020880826350610025 0.1610306494686017 chr7 159138663 3327900 0.02091195148472499 0.3828096687872425 chr8 146364022 4302152 0.029393507647664942 0.22360938756825383 chr9 141213431 2665460 0.018875400031885068 0.16248665004461146 chr10 135534747 3024209 0.02231316372324803 0.25628148479726315 chr11 135006516 1891398 0.01400967935503202 0.14622620967034128 chr12 133851895 2973286 0.022213252939003964 0.16589667156323196 chr13 115169878 1647092 0.014301413083028533 0.12576088816644823 chr14 107349540 2063254 0.01921996125926576 0.14804145704223523 chr15 102531392 1524086 0.014864579230524833 0.13067388680186778 chr16 90354753 1925441 0.021309792081441473 0.16034625979647116 chr17 81195210 2678774 0.032991773775817565 0.19736014690650044 chr18 78077248 1419055 0.018175013033246253 0.24460191354382865 chr19 59128983 1268883 0.021459577615261877 0.255118592756293 chr20 63025520 1422930 0.022577044981144146 0.16299090657404208 chr21 48129895 488782 0.010155476133908043 0.11284935953728269 chr22 51304566 955303 0.018620233528532332 0.14448423547999473 chrMT 16571 57278 3.456520427252429 2.658825004340296 chrX 155270560 2282960 0.014703109204990308 0.14390260634177227 chrY 59373566 135615 0.0022840972698186936 0.06566566442008068