BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524651.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 = 2,970,624 number of mapped reads = 2,743,624 (92.36%) number of supplementary alignments = 9,845 (0.33%) number of secondary alignments = 0 number of mapped bases = 160,637,451 bp number of sequenced bases = 160,587,927 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 336,543 duplication rate = 8.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9646 >>>>>>> ACTG content number of A's = 39,563,260 bp (24.64%) number of C's = 31,704,965 bp (19.74%) number of T's = 49,969,929 bp (31.12%) number of G's = 39,348,557 bp (24.5%) number of N's = 1,216 bp (0%) GC percentage = 44.25% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 813,933 number of insertions = 9,342 mapped reads with insertion percentage = 0.34% number of deletions = 29,341 mapped reads with deletion percentage = 1.06% homopolymer indels = 43.74% >>>>>>> Coverage mean coverageData = 0.0519X std coverageData = 0.4695X There is a 3.72% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 15817845 0.0634616071829165 0.8138103824047719 chr2 243199373 14225869 0.05849467794474947 0.6118480625564428 chr3 198022430 9949536 0.050244489980251224 0.29723765322825163 chr4 191154276 7391233 0.03866632311170481 0.4013697905038994 chr5 180915260 9734828 0.0538087721290067 0.3102165185198814 chr6 171115067 10377198 0.06064456030631131 0.3473725287857162 chr7 159138663 9619288 0.060445952093992394 0.53437445574585 chr8 146364022 14179665 0.0968794435014911 0.6684249160889164 chr9 141213431 5935228 0.042030194705771295 0.36728125679470114 chr10 135534747 7107829 0.05244285437740921 0.5875603233228018 chr11 135006516 8191905 0.060677849060263134 0.40297095031338215 chr12 133851895 5415658 0.04046007716215 0.27748708308206654 chr13 115169878 3796717 0.03296623271581481 0.2432078245953854 chr14 107349540 2899861 0.027013259674890083 0.22681082824864368 chr15 102531392 4208616 0.04104709706857389 0.26987369099772984 chr16 90354753 4814505 0.05328446861007965 0.33204688048833964 chr17 81195210 3686498 0.045402899998657556 0.30257425845184105 chr18 78077248 4205485 0.05386313052427258 0.6248032159643857 chr19 59128983 3406229 0.057606757755329564 0.5824477335709942 chr20 63025520 3182985 0.05050311365935577 0.32069927090695904 chr21 48129895 1484537 0.030844384763357578 0.33649501563333517 chr22 51304566 3145049 0.06130154185496862 0.3389111359131432 chrMT 16571 13147 0.7933739665681009 1.199231493032854 chrX 155270560 7300285 0.04701654325198544 0.3215010414680246 chrY 59373566 547455 0.009220517426896677 0.3803594582772304