BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084788.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,837,008 number of mapped reads = 1,665,038 (90.64%) number of supplementary alignments = 16,164 (0.88%) number of secondary alignments = 0 number of mapped bases = 113,276,343 bp number of sequenced bases = 113,233,369 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,612 duplication rate = 3.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4648 >>>>>>> ACTG content number of A's = 32,054,116 bp (28.31%) number of C's = 20,960,894 bp (18.51%) number of T's = 35,718,374 bp (31.54%) number of G's = 24,452,061 bp (21.59%) number of N's = 47,924 bp (0.04%) GC percentage = 40.11% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 942,825 number of insertions = 8,927 mapped reads with insertion percentage = 0.53% number of deletions = 26,402 mapped reads with deletion percentage = 1.57% homopolymer indels = 47.97% >>>>>>> Coverage mean coverageData = 0.0366X std coverageData = 0.296X There is a 3.12% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.06% 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 8887628 0.03565739561387091 0.4516890932038172 chr2 243199373 10027027 0.04122965810442283 0.3495541011972253 chr3 198022430 7527417 0.03801295136111601 0.22124571557416078 chr4 191154276 7786131 0.04073218325495371 0.23711670895577205 chr5 180915260 6707898 0.03707756880210105 0.21975295025588845 chr6 171115067 7135491 0.041699957374297145 0.26843387533985125 chr7 159138663 5856500 0.03680123918095252 0.3108307438066605 chr8 146364022 5519084 0.037707927976999706 0.36502219586280155 chr9 141213431 4983988 0.035294008259030264 0.28659124224232374 chr10 135534747 5092383 0.03757252743460686 0.30946028067971443 chr11 135006516 4979701 0.03688489376320177 0.275849878533446 chr12 133851895 5404203 0.04037449749964317 0.22985759607674874 chr13 115169878 3727365 0.03236406137375608 0.20650843117903162 chr14 107349540 3518633 0.03277734585541773 0.22253021273541443 chr15 102531392 3164660 0.030865278801637648 0.2045145718528644 chr16 90354753 2984581 0.033031809627103954 0.2259133999877436 chr17 81195210 3023348 0.03723554628407267 0.2372214489031564 chr18 78077248 3014827 0.03861338709069254 0.5580373972911474 chr19 59128983 1896233 0.03206943369886812 0.3349220301894288 chr20 63025520 2092212 0.03319626716288894 0.21462155652891407 chr21 48129895 1645279 0.03418413856917826 0.21875276127068413 chr22 51304566 1221591 0.023810570778437148 0.1737201490846606 chrMT 16571 7889 0.47607265705147545 0.8452503100770606 chrX 155270560 6799480 0.04379117329131807 0.25462942696113733 chrY 59373566 272794 0.004594536228462343 0.10835092440684545