BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251068.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP224945/SRP224945.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 = 4,451,915 number of mapped reads = 4,204,179 (94.44%) number of supplementary alignments = 30,435 (0.68%) number of secondary alignments = 0 number of mapped bases = 326,514,147 bp number of sequenced bases = 326,313,046 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 961,671 duplication rate = 20.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.1378 >>>>>>> ACTG content number of A's = 94,287,653 bp (28.89%) number of C's = 65,446,609 bp (20.06%) number of T's = 96,126,747 bp (29.46%) number of G's = 70,449,228 bp (21.59%) number of N's = 2,809 bp (0%) GC percentage = 41.65% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 1,874,220 number of insertions = 39,957 mapped reads with insertion percentage = 0.93% number of deletions = 111,746 mapped reads with deletion percentage = 2.61% homopolymer indels = 45.36% >>>>>>> Coverage mean coverageData = 0.1055X std coverageData = 1.1651X There is a 6.72% of reference with a coverageData >= 1X There is a 2.2% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 27107142 0.10875456153828399 2.491849858117565 chr2 243199373 28378858 0.11668968406427593 1.5516590756768984 chr3 198022430 21583646 0.10899596576004042 0.4793830496298303 chr4 191154276 19835591 0.10376744593461253 0.572878249345694 chr5 180915260 19407197 0.10727230527706728 0.5032769755375242 chr6 171115067 18634297 0.10889921809164824 0.6578928866545289 chr7 159138663 17840773 0.11210835043901306 1.6249287476303684 chr8 146364022 15939065 0.10890015717113868 0.7062328472807412 chr9 141213431 14054092 0.09952376272197508 1.2445874680436846 chr10 135534747 19279457 0.14224733824160973 1.1035020817578671 chr11 135006516 14870825 0.1101489427369565 0.6834537652218621 chr12 133851895 14985709 0.11195739141384588 0.5060637076241222 chr13 115169878 9302207 0.08076944389921122 0.40617079848875337 chr14 107349540 9991048 0.09307024510771075 0.7589035621435769 chr15 102531392 10003299 0.09756328091205473 0.452802493441049 chr16 90354753 9328129 0.10323894084465042 0.9495856931991307 chr17 81195210 9453460 0.11642878933375503 0.6174508586342192 chr18 78077248 8148612 0.1043660247861195 1.3758280235831888 chr19 59128983 7132782 0.12063089263686473 2.4000693582109616 chr20 63025520 6906285 0.10957918316262999 0.5463632529055259 chr21 48129895 3953798 0.08214848588387737 0.46206925979407826 chr22 51304566 4204291 0.08194769642920281 0.45416954034251006 chrMT 16571 271962 16.411924446321887 9.943008679484391 chrX 155270560 14982217 0.09649103474605875 0.5560657129945216 chrY 59373566 919405 0.015485089778841984 1.0785981936199975