BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716100.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 = 633,843 number of mapped reads = 563,899 (88.97%) number of supplementary alignments = 2,460 (0.39%) number of secondary alignments = 0 number of mapped bases = 32,422,246 bp number of sequenced bases = 32,412,792 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,765 duplication rate = 1.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5894 >>>>>>> ACTG content number of A's = 7,814,116 bp (24.11%) number of C's = 5,908,840 bp (18.23%) number of T's = 10,545,037 bp (32.53%) number of G's = 8,144,343 bp (25.13%) number of N's = 456 bp (0%) GC percentage = 43.36% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 164,681 number of insertions = 1,858 mapped reads with insertion percentage = 0.33% number of deletions = 6,014 mapped reads with deletion percentage = 1.06% homopolymer indels = 44.22% >>>>>>> Coverage mean coverageData = 0.0105X std coverageData = 0.1267X There is a 0.99% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% 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 2618779 0.01050660973077375 0.19451129740260034 chr2 243199373 2723729 0.011199572459424063 0.1538180466044731 chr3 198022430 2182874 0.011023367403379506 0.10905208044988667 chr4 191154276 2051418 0.010731740052731021 0.11105525863554787 chr5 180915260 1965598 0.010864744079631537 0.10881697101984816 chr6 171115067 1863523 0.010890467056299606 0.11518136784836688 chr7 159138663 1787345 0.011231368708935301 0.1422813869320934 chr8 146364022 1634034 0.011164178038234013 0.12183450080599283 chr9 141213431 1363090 0.009652693729961139 0.11258054681457848 chr10 135534747 1554186 0.011467066817928247 0.12903301009480292 chr11 135006516 1452112 0.010755866035384544 0.11760391536937914 chr12 133851895 1453057 0.010855707347288584 0.10880545700970709 chr13 115169878 1003178 0.008710419924209697 0.0967147950180686 chr14 107349540 961294 0.008954803159845865 0.09970380374541563 chr15 102531392 952259 0.009287487289746344 0.10131226885483259 chr16 90354753 953503 0.010552881484829028 0.10889215397604872 chr17 81195210 905871 0.01115670493370237 0.11217229868824669 chr18 78077248 850957 0.010898911293594774 0.15246330617768047 chr19 59128983 692681 0.011714745711083852 0.15067533743851266 chr20 63025520 701720 0.011133902584223025 0.11022067855608925 chr21 48129895 422562 0.008779616078530818 0.1021764254090246 chr22 51304566 399318 0.007783283850408169 0.09170015323076791 chrMT 16571 1659 0.10011465813771046 0.3200037133698403 chrX 155270560 1819831 0.011720386659261098 0.1166106593817806 chrY 59373566 107668 0.001813399585936947 0.06097362642447742