BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716560.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 = 24,975,509 number of mapped reads = 24,407,764 (97.73%) number of supplementary alignments = 19,969 (0.08%) number of secondary alignments = 0 number of mapped bases = 1,657,899,146 bp number of sequenced bases = 1,657,616,039 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,405,763 duplication rate = 1.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.7419 >>>>>>> ACTG content number of A's = 465,368,576 bp (28.07%) number of C's = 357,354,868 bp (21.56%) number of T's = 484,062,111 bp (29.2%) number of G's = 350,747,420 bp (21.16%) number of N's = 83,064 bp (0.01%) GC percentage = 42.72% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 5,031,691 number of insertions = 139,166 mapped reads with insertion percentage = 0.57% number of deletions = 133,420 mapped reads with deletion percentage = 0.54% homopolymer indels = 35.62% >>>>>>> Coverage mean coverageData = 0.5356X std coverageData = 5.6579X There is a 36.72% of reference with a coverageData >= 1X There is a 10.5% of reference with a coverageData >= 2X There is a 2.65% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 160793908 0.6451093576212193 10.186097986708536 chr2 243199373 129118037 0.5309143498490845 4.059977113468862 chr3 198022430 89461133 0.45177272594826756 2.782446676531036 chr4 191154276 93569527 0.48949743086050557 3.85146711275238 chr5 180915260 88905360 0.4914199056508555 0.9461166661840776 chr6 171115067 70925973 0.4144928570200075 2.099194300965606 chr7 159138663 80502018 0.5058608416233835 3.5295469150862164 chr8 146364022 139815356 0.9552576793769715 2.054370813948859 chr9 141213431 68226600 0.48314526116145423 3.2727651247911176 chr10 135534747 97769879 0.7213639392413519 17.042414880411147 chr11 135006516 58561532 0.43376818938131845 1.925686567575435 chr12 133851895 73989834 0.5527738998390721 0.9813225288698424 chr13 115169878 37436653 0.3250559404083071 0.7046921547703178 chr14 107349540 39003627 0.36333296817107924 0.865638902395483 chr15 102531392 43043951 0.4198124121829927 0.7305880415671293 chr16 90354753 59387334 0.6572685113753783 5.421858872433642 chr17 81195210 59387061 0.7314108923420483 1.907415553332596 chr18 78077248 38786021 0.496764704104325 5.145392172077098 chr19 59128983 34959394 0.591239561823683 7.066905962885582 chr20 63025520 47622730 0.7556102670791134 1.5462676144993557 chr21 48129895 23430283 0.4868135074884331 3.5768849414019184 chr22 51304566 15634613 0.3047411608549617 0.8955150771387055 chrMT 16571 11060470 667.4594170538893 202.38381657059185 chrX 155270560 88122477 0.5675414386346002 1.3642889391254993 chrY 59373566 8385375 0.14123077936737033 6.4342467185247045