BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524612.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 = 1,899,292 number of mapped reads = 1,767,857 (93.08%) number of supplementary alignments = 3,843 (0.2%) number of secondary alignments = 0 number of mapped bases = 103,097,248 bp number of sequenced bases = 103,063,571 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,767 duplication rate = 3.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5339 >>>>>>> ACTG content number of A's = 26,262,746 bp (25.48%) number of C's = 19,967,799 bp (19.37%) number of T's = 32,366,977 bp (31.4%) number of G's = 24,465,354 bp (23.74%) number of N's = 695 bp (0%) GC percentage = 43.11% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 486,846 number of insertions = 6,927 mapped reads with insertion percentage = 0.39% number of deletions = 19,754 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.63% >>>>>>> Coverage mean coverageData = 0.0333X std coverageData = 0.282X There is a 2.9% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 10775659 0.043232225287013426 0.48290443485610846 chr2 243199373 8563143 0.035210382717557415 0.3304419916821609 chr3 198022430 7305925 0.03689443160555095 0.2165206019997845 chr4 191154276 4646480 0.024307486587430562 0.19901736215401458 chr5 180915260 6262700 0.03461675924960669 0.2089799244617805 chr6 171115067 6378257 0.03727466617536374 0.2308530499274015 chr7 159138663 6215518 0.039057246572443555 0.36018483373586885 chr8 146364022 9024533 0.06165813754421151 0.37848354520242694 chr9 141213431 3599691 0.025491137595828262 0.2514831649536574 chr10 135534747 4469438 0.03297632598967407 0.2788296613632434 chr11 135006516 5362900 0.03972326787545573 0.27700972256674383 chr12 133851895 3369934 0.025176587899633396 0.18390532323108388 chr13 115169878 2421603 0.021026357256365244 0.16592978130449804 chr14 107349540 1865666 0.017379357191470032 0.15652482434248174 chr15 102531392 2615512 0.02550937765479669 0.1914540395274993 chr16 90354753 3140497 0.03475740783664142 0.2202441716792323 chr17 81195210 2587475 0.03186733552385664 0.20664042301944854 chr18 78077248 2635757 0.0337583235515678 0.38500557810504094 chr19 59128983 2145557 0.03628604604953209 0.3653385721648851 chr20 63025520 1949680 0.03093477055008828 0.2012959844255418 chr21 48129895 903769 0.018777705623500736 0.16694935946867026 chr22 51304566 2063019 0.040211216288234465 0.22641363745685122 chrMT 16571 10217 0.6165590489409208 0.9541924046390979 chrX 155270560 4551228 0.02931159648036305 0.2155213164211237 chrY 59373566 233090 0.003925821130568442 0.11241857091629372