BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506021.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 5,626,778 number of mapped reads = 3,899,973 (69.31%) number of supplementary alignments = 196 (0%) number of secondary alignments = 0 number of mapped bases = 180,129,538 bp number of sequenced bases = 180,093,481 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 263,531 duplication rate = 5.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5976 >>>>>>> ACTG content number of A's = 52,819,232 bp (29.33%) number of C's = 36,883,199 bp (20.48%) number of T's = 52,417,185 bp (29.11%) number of G's = 37,379,392 bp (20.76%) number of N's = 594,473 bp (0.33%) GC percentage = 41.24% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,443,912 number of insertions = 7,740 mapped reads with insertion percentage = 0.2% number of deletions = 26,066 mapped reads with deletion percentage = 0.67% homopolymer indels = 44.5% >>>>>>> Coverage mean coverageData = 0.0582X std coverageData = 0.5988X There is a 4.36% of reference with a coverageData >= 1X There is a 0.97% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 17747916 0.07120510243382704 1.2901049817067616 chr2 243199373 10728991 0.04411603067743106 0.39830367621687485 chr3 198022430 10827269 0.05467698280442271 0.29942666793433836 chr4 191154276 7615119 0.039837555085610536 0.2593175296312088 chr5 180915260 12602871 0.06966173555508806 0.33998982498904695 chr6 171115067 12324213 0.07202295634200348 0.3973773545364381 chr7 159138663 11322348 0.07114768835276691 0.9912833490049013 chr8 146364022 10813753 0.07388258980748698 0.692416856567127 chr9 141213431 8497565 0.06017533133941062 0.40739761861965296 chr10 135534747 5644218 0.041644066373621516 0.49075899409874707 chr11 135006516 9232095 0.06838258828929412 0.4404507767871263 chr12 133851895 5070710 0.03788299000174783 0.26887167061701533 chr13 115169878 5901024 0.051237564044306794 0.2859700795000041 chr14 107349540 6348000 0.05913392828697729 0.9508858229656636 chr15 102531392 5967636 0.05820301357071208 0.30673134988194045 chr16 90354753 5716489 0.0632671642630687 0.36190586186203183 chr17 81195210 2876373 0.03542540255761393 0.2569472735304734 chr18 78077248 5591772 0.07161845663412726 0.6766649045418663 chr19 59128983 4548992 0.076933371236911 0.8884850250576752 chr20 63025520 4411873 0.07000137404657669 0.3493762787727683 chr21 48129895 2597692 0.053972525807504876 0.32081452766512486 chr22 51304566 1263455 0.02462656052874514 0.19736450447535062 chrMT 16571 134120 8.093657594592964 6.345278906148149 chrX 155270560 11774814 0.07583416972283735 0.40257735156342783 chrY 59373566 570230 0.009604105638526074 0.16497461444086872