BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524858.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 = 1,137,510 number of mapped reads = 1,048,566 (92.18%) number of supplementary alignments = 6,764 (0.59%) number of secondary alignments = 0 number of mapped bases = 61,422,492 bp number of sequenced bases = 61,404,683 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,925 duplication rate = 1.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4021 >>>>>>> ACTG content number of A's = 15,185,044 bp (24.73%) number of C's = 11,374,765 bp (18.52%) number of T's = 19,671,085 bp (32.04%) number of G's = 15,165,522 bp (24.7%) number of N's = 8,267 bp (0.01%) GC percentage = 43.22% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 290,180 number of insertions = 4,034 mapped reads with insertion percentage = 0.38% number of deletions = 11,364 mapped reads with deletion percentage = 1.08% homopolymer indels = 44.18% >>>>>>> Coverage mean coverageData = 0.0198X std coverageData = 0.2133X There is a 1.85% 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 5213860 0.020918142466734315 0.39496864592051434 chr2 243199373 3976814 0.016352073407689256 0.21053444181690117 chr3 198022430 4482008 0.022633840014992242 0.1574616506547389 chr4 191154276 3328809 0.01741425339603703 0.14518738467795123 chr5 180915260 3475440 0.0192103197928135 0.1453745733947973 chr6 171115067 4043585 0.023630794592740333 0.17326337713100304 chr7 159138663 2834395 0.017810850905540156 0.2793939181730345 chr8 146364022 6597795 0.04507798371378453 0.2886762609865924 chr9 141213431 2523071 0.017867075264250184 0.18334185595335897 chr10 135534747 3147002 0.023219152797769267 0.21060639910188034 chr11 135006516 2958525 0.02191394228705228 0.19041237089752658 chr12 133851895 2466544 0.018427411879376084 0.14464321286372336 chr13 115169878 1600247 0.013894666103579619 0.12265000540651175 chr14 107349540 1310177 0.012204775167178173 0.12481561720155862 chr15 102531392 1825756 0.01780680008713819 0.1420760795148463 chr16 90354753 1791208 0.01982417017951452 0.15691256448347987 chr17 81195210 1755583 0.02162175576613448 0.16993377700247694 chr18 78077248 1467039 0.01878958387467755 0.3211781223872374 chr19 59128983 960642 0.016246550359237534 0.28378679951769187 chr20 63025520 1318556 0.020920985657873193 0.15350557161523581 chr21 48129895 788358 0.016379798875522166 0.14085194319375655 chr22 51304566 379755 0.00740197276008533 0.08938806569410733 chrMT 16571 1469 0.08864884436666466 0.31619673975003926 chrX 155270560 3016308 0.019426142341471556 0.161576523870525 chrY 59373566 159546 0.002687155425362189 0.07730940887299734