BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524530.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 = 1,085,077 number of mapped reads = 996,708 (91.86%) number of supplementary alignments = 4,403 (0.41%) number of secondary alignments = 0 number of mapped bases = 58,234,575 bp number of sequenced bases = 58,216,315 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,445 duplication rate = 3.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6443 >>>>>>> ACTG content number of A's = 14,015,089 bp (24.07%) number of C's = 10,923,175 bp (18.76%) number of T's = 18,734,409 bp (32.18%) number of G's = 14,542,805 bp (24.98%) number of N's = 837 bp (0%) GC percentage = 43.74% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 300,768 number of insertions = 3,829 mapped reads with insertion percentage = 0.38% number of deletions = 10,921 mapped reads with deletion percentage = 1.09% homopolymer indels = 44.09% >>>>>>> Coverage mean coverageData = 0.0188X std coverageData = 0.2011X There is a 1.69% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 4593357 0.018428668227871738 0.34878304665479626 chr2 243199373 4958107 0.02038700568524903 0.22919231702967535 chr3 198022430 3833284 0.019357827292595085 0.15129202827592705 chr4 191154276 3741983 0.01957572217741025 0.17303175896065176 chr5 180915260 3483477 0.019254743906069616 0.15067953069439952 chr6 171115067 3385553 0.01978524193898133 0.1679728147207851 chr7 159138663 3155359 0.019827733503077125 0.233373381268395 chr8 146364022 3021083 0.020640885367307002 0.21195158310019654 chr9 141213431 2416750 0.017114165294942803 0.17147318396925484 chr10 135534747 2886690 0.021298523543929294 0.2133062747453432 chr11 135006516 2621438 0.019417122059501187 0.18245507000981773 chr12 133851895 2635637 0.01969069619821221 0.15380805580331242 chr13 115169878 1846558 0.016033341634693752 0.1373121739195813 chr14 107349540 1745349 0.01625856058628663 0.14112744238833233 chr15 102531392 1657958 0.016170247644740843 0.13787757034116396 chr16 90354753 1667164 0.018451314896516843 0.15636429523047957 chr17 81195210 1562173 0.01923971869769165 0.15631590433648912 chr18 78077248 1579640 0.020231758168525613 0.2931304177747493 chr19 59128983 1154135 0.01951893879182735 0.24412646988186715 chr20 63025520 1259471 0.01998350826776201 0.15621772499416944 chr21 48129895 782017 0.016248051237178058 0.16058379087140132 chr22 51304566 686879 0.0133882625573716 0.1264855777774664 chrMT 16571 7373 0.44493392070484583 0.7538248457389932 chrX 155270560 3341301 0.021519217809222817 0.16805948553663136 chrY 59373566 211839 0.003567900907282544 0.131231423635396