BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524767.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 = 1,419,786 number of mapped reads = 1,306,591 (92.03%) number of supplementary alignments = 4,568 (0.32%) number of secondary alignments = 0 number of mapped bases = 75,909,127 bp number of sequenced bases = 75,885,047 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,185 duplication rate = 2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3314 >>>>>>> ACTG content number of A's = 18,676,580 bp (24.61%) number of C's = 14,020,429 bp (18.48%) number of T's = 24,605,368 bp (32.42%) number of G's = 18,581,089 bp (24.49%) number of N's = 1,581 bp (0%) GC percentage = 42.96% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 385,663 number of insertions = 6,141 mapped reads with insertion percentage = 0.47% number of deletions = 15,188 mapped reads with deletion percentage = 1.16% homopolymer indels = 40.9% >>>>>>> Coverage mean coverageData = 0.0245X std coverageData = 0.2397X There is a 2.25% 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 6341918 0.02544394061910883 0.38897830118728355 chr2 243199373 6044013 0.024852091209955546 0.31637064382019087 chr3 198022430 4418913 0.022315214493630848 0.16084811886781886 chr4 191154276 4711057 0.02464531319194764 0.18533089190955665 chr5 180915260 4398754 0.02431389148709733 0.1665577006611202 chr6 171115067 4056907 0.023708648637001672 0.19043461157023006 chr7 159138663 4335547 0.027243832003288854 0.3280766511211297 chr8 146364022 4064799 0.02777184546076494 0.2964157638325851 chr9 141213431 2489297 0.017627905379623558 0.17162843021680665 chr10 135534747 3384945 0.024974739503516395 0.2583956714373019 chr11 135006516 2680915 0.019857671166034683 0.19208969337660597 chr12 133851895 3771223 0.028174595510956343 0.17974187424683805 chr13 115169878 2288023 0.019866505372177264 0.15138121676846758 chr14 107349540 2544538 0.023703296725817363 0.1655936021579874 chr15 102531392 2757674 0.026895899355389614 0.17749477867141703 chr16 90354753 2547976 0.02819968972744577 0.19014032728877375 chr17 81195210 3216595 0.03961557584492977 0.22093426410659558 chr18 78077248 1433857 0.018364594510298315 0.2813649045837867 chr19 59128983 1872150 0.031662137669440385 0.29739253739185134 chr20 63025520 2383400 0.037816427377354446 0.2152335979466908 chr21 48129895 974026 0.020237442861655942 0.16771823301640038 chr22 51304566 664021 0.012942727163894146 0.12069132882720887 chrMT 16571 84339 5.089554040190695 3.477528876778723 chrX 155270560 4180656 0.0269249753462601 0.18763562288830873 chrY 59373566 263584 0.004439416692606942 0.16943060593296688