BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472622.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 16,428,788 number of mapped reads = 16,293,837 (99.18%) number of supplementary alignments = 85,638 (0.52%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,169,331 number of mapped paired reads (second in pair) = 8,124,506 number of mapped paired reads (both in pair) = 16,202,572 number of mapped paired reads (singletons) = 91,265 number of mapped bases = 1,604,579,107 bp number of sequenced bases = 1,604,362,689 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,150,612 duplication rate = 49.62% >>>>>>> Insert size mean insert size = 20,473.5778 std insert size = 1,413,404.0263 median insert size = 226 >>>>>>> Mapping quality mean mapping quality = 54.6441 >>>>>>> ACTG content number of A's = 428,874,108 bp (26.73%) number of C's = 375,475,235 bp (23.4%) number of T's = 429,748,260 bp (26.79%) number of G's = 369,970,998 bp (23.06%) number of N's = 294,088 bp (0.02%) GC percentage = 46.46% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 10,117,528 number of insertions = 99,550 mapped reads with insertion percentage = 0.6% number of deletions = 91,595 mapped reads with deletion percentage = 0.56% homopolymer indels = 46.18% >>>>>>> Coverage mean coverageData = 0.5183X std coverageData = 22.1528X There is a 3.44% of reference with a coverageData >= 1X There is a 1.58% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 233691493 0.937576372176822 30.958624725328804 chr2 243199373 88837248 0.3652856785942454 17.420579463201186 chr3 198022430 124759295 0.630026078358901 18.25152126823979 chr4 191154276 41189306 0.21547677018744796 15.01437802427398 chr5 180915260 50561567 0.27947651845399885 12.34638899623858 chr6 171115067 102244991 0.5975218476815954 17.233943855715694 chr7 159138663 106136281 0.6669421434060936 40.889859981429225 chr8 146364022 92291763 0.6305631789757732 22.086307217690177 chr9 141213431 77960986 0.552079114910819 16.394405834785108 chr10 135534747 29791613 0.21980793604167057 12.030458567919199 chr11 135006516 42638339 0.31582430436172426 14.354773446176553 chr12 133851895 68115445 0.5088866691054318 16.522691635858003 chr13 115169878 35562288 0.30878115543371504 10.152178831244967 chr14 107349540 43173318 0.4021751560369984 17.16402433307337 chr15 102531392 37168235 0.3625059045331209 17.71834352626609 chr16 90354753 91350615 1.0110216891412453 31.991664520305672 chr17 81195210 77991359 0.960541379226681 24.594428175421804 chr18 78077248 16143613 0.20676462623272787 6.717951601084203 chr19 59128983 50364106 0.8517668230485209 35.62544067001218 chr20 63025520 78206404 1.240868841700949 48.37231960048596 chr21 48129895 10211111 0.21215735043677117 13.076101169218408 chr22 51304566 42589489 0.830130577461663 38.76393631796055 chrMT 16571 2375 0.14332267213807254 0.48628580000595795 chrX 155270560 62893318 0.40505629657032216 14.079087136872486 chrY 59373566 704549 0.01186637501274557 0.37989966489557553