BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081156.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 = 3,144,217 number of mapped reads = 2,781,857 (88.48%) number of supplementary alignments = 28,724 (0.91%) number of secondary alignments = 0 number of mapped bases = 186,613,347 bp number of sequenced bases = 186,542,794 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 130,933 duplication rate = 3.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5473 >>>>>>> ACTG content number of A's = 52,680,669 bp (28.24%) number of C's = 34,464,659 bp (18.48%) number of T's = 58,609,571 bp (31.42%) number of G's = 40,733,339 bp (21.84%) number of N's = 54,556 bp (0.03%) GC percentage = 40.31% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,588,616 number of insertions = 14,950 mapped reads with insertion percentage = 0.53% number of deletions = 43,755 mapped reads with deletion percentage = 1.56% homopolymer indels = 46.82% >>>>>>> Coverage mean coverageData = 0.0603X std coverageData = 0.4906X There is a 5.02% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 14428719 0.057888397397413104 0.6598202801301031 chr2 243199373 14948887 0.06146762146463264 0.6008681255578159 chr3 198022430 13073112 0.06601833943760815 0.295902291801084 chr4 191154276 12706028 0.06647001712899166 0.3169128975763053 chr5 180915260 11190689 0.061855970579817315 0.2903303251212287 chr6 171115067 12697345 0.07420354748772649 0.5430181697877932 chr7 159138663 11068146 0.06955032668585383 0.9189504155820324 chr8 146364022 8569360 0.05854826809828989 0.5940757107455489 chr9 141213431 7509644 0.053179389147481305 0.44270940183004215 chr10 135534747 9661593 0.07128498937619296 0.44401514729734276 chr11 135006516 8219735 0.060883987258807566 0.5139533167303686 chr12 133851895 8873382 0.06629253922777859 0.30426000620368027 chr13 115169878 6253440 0.05429753081791056 0.26777078610727834 chr14 107349540 6256883 0.05828514029962308 0.2986245020575187 chr15 102531392 5279502 0.05149156660235336 0.2718267216164731 chr16 90354753 4349484 0.04813785501687996 0.30651744582975876 chr17 81195210 4343645 0.05349632078049924 0.32570031964927465 chr18 78077248 4937213 0.0632349772369026 0.9297898914780341 chr19 59128983 2474802 0.041854296732957506 0.4951826893616214 chr20 63025520 3468344 0.05503078752860746 0.2827039621465783 chr21 48129895 2310397 0.048003366722491295 0.28279904928755617 chr22 51304566 1990832 0.038804187525921185 0.22398391679913435 chrMT 16571 45955 2.7732182728863677 2.340681712900036 chrX 155270560 11455222 0.0737758786984474 0.35410723559154833 chrY 59373566 500988 0.008437896420100488 0.1800358727706192