BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819035.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,855,305 number of mapped reads = 1,657,692 (89.35%) number of supplementary alignments = 7,414 (0.4%) number of secondary alignments = 0 number of mapped bases = 94,172,219 bp number of sequenced bases = 94,147,592 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,040 duplication rate = 2.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8813 >>>>>>> ACTG content number of A's = 22,970,998 bp (24.4%) number of C's = 18,911,522 bp (20.09%) number of T's = 30,312,462 bp (32.2%) number of G's = 21,950,544 bp (23.32%) number of N's = 2,066 bp (0%) GC percentage = 43.4% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 466,297 number of insertions = 5,584 mapped reads with insertion percentage = 0.34% number of deletions = 14,733 mapped reads with deletion percentage = 0.88% homopolymer indels = 40.97% >>>>>>> Coverage mean coverageData = 0.0304X std coverageData = 0.2366X There is a 2.73% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% 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 10629110 0.04264426687225786 0.33933196410034 chr2 243199373 7876938 0.03238880883134514 0.27503998262179136 chr3 198022430 6250768 0.031565959472368864 0.19477353532883976 chr4 191154276 6049283 0.03164607732865991 0.20943639563739605 chr5 180915260 4643472 0.02566655792330619 0.17700587628127698 chr6 171115067 4930503 0.028813961776960294 0.19571374749538167 chr7 159138663 4122740 0.02590658939996247 0.20709749467286898 chr8 146364022 5896713 0.040287995092127216 0.2489901763945663 chr9 141213431 3392302 0.02402251666840387 0.24457237080271524 chr10 135534747 4438700 0.03274953543831827 0.26964370810306315 chr11 135006516 2922908 0.02165012539098483 0.21609805889199532 chr12 133851895 4188183 0.03128968028431723 0.19554120469391145 chr13 115169878 2904794 0.025221820587497713 0.1715004554519553 chr14 107349540 3299903 0.03073979636987732 0.20574674123636347 chr15 102531392 2704679 0.026379033262320287 0.17703321437357458 chr16 90354753 2860147 0.03165463802441029 0.21430396666835244 chr17 81195210 2146498 0.026436263912612577 0.18498147671686957 chr18 78077248 2312145 0.02961355656387889 0.42606996805088965 chr19 59128983 1821265 0.03080156139333565 0.2787987430290982 chr20 63025520 2924556 0.046402727022323655 0.24161730502868606 chr21 48129895 1222347 0.02539683496089073 0.1946179631105244 chr22 51304566 1121369 0.021857099424639904 0.1608683635970574 chrMT 16571 2018 0.12177901152616016 0.3692590862954289 chrX 155270560 5243088 0.0337674315079433 0.22618668991527746 chrY 59373566 267790 0.004510256298232112 0.10646688623679498