BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525247.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 = 891,723 number of mapped reads = 810,661 (90.91%) number of supplementary alignments = 2,745 (0.31%) number of secondary alignments = 0 number of mapped bases = 46,675,955 bp number of sequenced bases = 46,661,647 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,944 duplication rate = 2.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7112 >>>>>>> ACTG content number of A's = 11,557,982 bp (24.77%) number of C's = 7,619,738 bp (16.33%) number of T's = 15,343,819 bp (32.88%) number of G's = 12,139,200 bp (26.02%) number of N's = 908 bp (0%) GC percentage = 42.35% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 235,928 number of insertions = 3,342 mapped reads with insertion percentage = 0.41% number of deletions = 9,027 mapped reads with deletion percentage = 1.11% homopolymer indels = 45.1% >>>>>>> Coverage mean coverageData = 0.0151X std coverageData = 0.1714X There is a 1.4% of reference with a coverageData >= 1X There is a 0.08% 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 5042180 0.020229357823746404 0.2586787146751328 chr2 243199373 3941635 0.016207422541340187 0.2430099200383656 chr3 198022430 3451523 0.017429959828288138 0.1425352773140389 chr4 191154276 2063462 0.010794746752094627 0.11646988629110533 chr5 180915260 2102358 0.01162067810089652 0.11401254332722002 chr6 171115067 3066639 0.017921501909589296 0.15524975120120144 chr7 159138663 2881180 0.01810483980250607 0.23075440405114467 chr8 146364022 2715263 0.01855143745639895 0.18440146501776664 chr9 141213431 1555647 0.011016282155200945 0.132615575158547 chr10 135534747 2500891 0.0184520283938701 0.20417362099514022 chr11 135006516 2199781 0.0162938876224315 0.15165540348986287 chr12 133851895 2107659 0.015746202173678604 0.13424983930248283 chr13 115169878 1469519 0.012759577638868385 0.12002560247411766 chr14 107349540 1756048 0.01635822566170288 0.13661121817640973 chr15 102531392 1279757 0.012481611485387812 0.11949707187103731 chr16 90354753 1239771 0.013721148681575169 0.13571615475361307 chr17 81195210 829954 0.010221711354647644 0.10939814691333762 chr18 78077248 979492 0.012545165526325928 0.2121208622458396 chr19 59128983 722669 0.012221908163040788 0.1936545841271456 chr20 63025520 990888 0.0157220122896249 0.13371529434653734 chr21 48129895 598282 0.012430569399746249 0.12423657653511712 chr22 51304566 406252 0.007918437512949628 0.09373362461660929 chrMT 16571 42904 2.5891014422786798 2.066717773284055 chrX 155270560 2581692 0.016627054091902547 0.1440168308675634 chrY 59373566 150509 0.0025349496440890884 0.09076523160421138