BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714182.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 2,040,710 number of mapped reads = 1,909,718 (93.58%) number of supplementary alignments = 100,807 (4.94%) number of secondary alignments = 0 number of mapped bases = 242,889,180 bp number of sequenced bases = 238,088,583 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,815,109 duplication rate = 46.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.8109 >>>>>>> ACTG content number of A's = 70,892,320 bp (29.78%) number of C's = 48,213,307 bp (20.25%) number of T's = 66,230,343 bp (27.82%) number of G's = 52,750,772 bp (22.16%) number of N's = 1,841 bp (0%) GC percentage = 42.41% >>>>>>> Mismatches and indels general error rate = 0.0383 number of mismatches = 8,515,858 number of insertions = 246,160 mapped reads with insertion percentage = 12.52% number of deletions = 770,039 mapped reads with deletion percentage = 38.46% homopolymer indels = 26.66% >>>>>>> Coverage mean coverageData = 0.0785X std coverageData = 13.8377X There is a 0.1% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 16786344 0.06734725046081229 16.440433826500314 chr2 243199373 24520239 0.10082361108718813 19.557976882430214 chr3 198022430 13268654 0.06700581343234703 7.9541921232946615 chr4 191154276 14233489 0.07446074081021342 11.381253075907452 chr5 180915260 14253370 0.07878478576102425 12.46852269895525 chr6 171115067 12795961 0.07477986143674888 10.183080083495774 chr7 159138663 10713325 0.06732069252083638 9.770833631219293 chr8 146364022 10801816 0.07380103287951462 10.307212852941385 chr9 141213431 8117018 0.05748049560526576 7.584170970671795 chr10 135534747 10738463 0.07923033198269075 20.364373053973953 chr11 135006516 10257486 0.07597771058694679 12.92507381406832 chr12 133851895 10288926 0.0768679890561131 15.04484780446381 chr13 115169878 7072699 0.061411014084776575 8.263075477784962 chr14 107349540 8905419 0.0829572162116391 12.499513720713617 chr15 102531392 6430013 0.06271262756288337 9.653304734769005 chr16 90354753 3020275 0.033426852486664424 4.623318958667753 chr17 81195210 3249948 0.04002635130816214 6.307156687633313 chr18 78077248 4692055 0.06009503562420643 7.977591375898804 chr19 59128983 1210311 0.020468997411979842 3.1006233983792293 chr20 63025520 3949781 0.06266955036626433 11.279060824252975 chr21 48129895 1538123 0.03195774684320421 5.273070083618851 chr22 51304566 1147736 0.02237103028997458 3.198173701840115 chrMT 16571 118489 7.150383199565506 56.03821945826673 chrX 155270560 43216385 0.27832954940073634 30.542219050641755 chrY 59373566 1562855 0.026322404148674514 5.2168268167979805