BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818790.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 = 2,108,321 number of mapped reads = 2,050,242 (97.25%) number of supplementary alignments = 17,390 (0.82%) number of secondary alignments = 0 number of mapped bases = 139,083,793 bp number of sequenced bases = 139,025,333 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,131,793 duplication rate = 45.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7058 >>>>>>> ACTG content number of A's = 40,238,112 bp (28.94%) number of C's = 30,746,883 bp (22.12%) number of T's = 39,292,170 bp (28.26%) number of G's = 28,739,315 bp (20.67%) number of N's = 8,853 bp (0.01%) GC percentage = 42.79% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 720,006 number of insertions = 15,836 mapped reads with insertion percentage = 0.76% number of deletions = 36,192 mapped reads with deletion percentage = 1.75% homopolymer indels = 41.26% >>>>>>> Coverage mean coverageData = 0.0449X std coverageData = 0.6078X There is a 1.64% of reference with a coverageData >= 1X There is a 0.93% of reference with a coverageData >= 2X There is a 0.61% of reference with a coverageData >= 3X There is a 0.41% of reference with a coverageData >= 4X There is a 0.27% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 11679942 0.04686023229607119 0.7814538372817269 chr2 243199373 12262758 0.050422654666959194 0.9606317632543546 chr3 198022430 8860952 0.04474721373735289 0.4543181054399274 chr4 191154276 9343075 0.048877143611477464 0.5397836207217187 chr5 180915260 8471464 0.046825591163509366 0.4766280476511733 chr6 171115067 8307342 0.04854827891923743 0.5187786720987575 chr7 159138663 7649298 0.0480668736044364 0.5394096007782371 chr8 146364022 7132956 0.048734353583150376 0.5207751772962813 chr9 141213431 5942527 0.04208188242377597 0.5004197336794142 chr10 135534747 6758767 0.049867411491165435 0.6568334166004657 chr11 135006516 6428016 0.04761263523013956 0.5137492157572349 chr12 133851895 6229621 0.04654114908122892 0.5307200077084471 chr13 115169878 4605346 0.039987417543326735 0.43467733452093943 chr14 107349540 4409287 0.041074111728843926 0.48460567133776444 chr15 102531392 4227914 0.04123531259577554 0.447713397518416 chr16 90354753 4106116 0.04544438298669246 0.7370569101985422 chr17 81195210 3751904 0.046208440128426294 0.49897964046818355 chr18 78077248 3865866 0.04951334862622207 0.6612509900622275 chr19 59128983 2627698 0.04444010139663657 0.6479002805106089 chr20 63025520 3003559 0.047656235125073144 0.5126819552239269 chr21 48129895 1957677 0.04067486538252369 0.4580188822593042 chr22 51304566 1746183 0.03403562560104299 0.45120164835543497 chrMT 16571 146482 8.839659646370166 9.924734075625492 chrX 155270560 4258628 0.027427143947957682 0.39763033734682596 chrY 59373566 1310415 0.022070680410201403 1.0833840159582067