BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867864.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 = 1,867,628 number of mapped reads = 1,715,740 (91.87%) number of supplementary alignments = 7,536 (0.4%) number of secondary alignments = 0 number of mapped bases = 100,612,304 bp number of sequenced bases = 100,582,369 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,434 duplication rate = 3.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5802 >>>>>>> ACTG content number of A's = 25,857,393 bp (25.71%) number of C's = 18,695,798 bp (18.59%) number of T's = 32,340,344 bp (32.15%) number of G's = 23,675,425 bp (23.54%) number of N's = 13,409 bp (0.01%) GC percentage = 42.13% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 507,781 number of insertions = 7,681 mapped reads with insertion percentage = 0.45% number of deletions = 18,631 mapped reads with deletion percentage = 1.08% homopolymer indels = 41.9% >>>>>>> Coverage mean coverageData = 0.0325X std coverageData = 0.3064X There is a 2.89% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8083112 0.0324296564139754 0.5445441790217838 chr2 243199373 8644095 0.03554324541782433 0.4527923496335409 chr3 198022430 6587240 0.03326512052195299 0.20027398358099036 chr4 191154276 6495264 0.033979171881041256 0.23200657226647323 chr5 180915260 6138512 0.033930316325997044 0.2041357373771946 chr6 171115067 5843858 0.034151627337410326 0.23454677546292377 chr7 159138663 5413051 0.03401468190040028 0.3442437508918936 chr8 146364022 5131964 0.03506301569111021 0.30793832664170834 chr9 141213431 4265701 0.03020747367861914 0.25569959987966473 chr10 135534747 4799414 0.035410948898587605 0.30952233093415166 chr11 135006516 4603787 0.03410048000942414 0.2612267895712669 chr12 133851895 4530903 0.03385012218168446 0.2065572305458212 chr13 115169878 3107498 0.02698186412943843 0.18343740143204876 chr14 107349540 2981464 0.027773421292722818 0.19310876574104355 chr15 102531392 2879689 0.02808592513793239 0.18939227563074326 chr16 90354753 2910578 0.032212782431047096 0.21282524349584425 chr17 81195210 2760121 0.03399364322107178 0.2152992362119681 chr18 78077248 2671992 0.03422241521627402 0.45750420210960735 chr19 59128983 2127938 0.035988070351218454 0.396592352327589 chr20 63025520 2110152 0.03348091376318672 0.20552811640139568 chr21 48129895 1312858 0.027277391733349927 0.21322533241998734 chr22 51304566 1197247 0.023336071101351875 0.16757112213480366 chrMT 16571 9766 0.5893428278317543 0.8406584412540169 chrX 155270560 5682503 0.03659742709757729 0.2327913820383239 chrY 59373566 323597 0.005450186367448436 0.18477225789023816