BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505959.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 = 5,098,912 number of mapped reads = 3,579,185 (70.2%) number of supplementary alignments = 199 (0%) number of secondary alignments = 0 number of mapped bases = 167,084,289 bp number of sequenced bases = 167,051,971 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 270,478 duplication rate = 5.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1658 >>>>>>> ACTG content number of A's = 49,964,755 bp (29.91%) number of C's = 33,716,887 bp (20.18%) number of T's = 49,592,719 bp (29.69%) number of G's = 33,776,808 bp (20.22%) number of N's = 802 bp (0%) GC percentage = 40.4% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 852,525 number of insertions = 7,893 mapped reads with insertion percentage = 0.22% number of deletions = 23,827 mapped reads with deletion percentage = 0.66% homopolymer indels = 44.12% >>>>>>> Coverage mean coverageData = 0.054X std coverageData = 0.6053X There is a 4.14% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% 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 12052127 0.0483534482347388 0.9340181009487653 chr2 243199373 12499807 0.05139736523909542 0.4177054351430646 chr3 198022430 11218572 0.05665303672922305 0.2986596788889797 chr4 191154276 11716143 0.061291555936734576 0.3109921329540569 chr5 180915260 11126140 0.06149917922899373 0.32026642860893656 chr6 171115067 9425369 0.0550820518920172 0.41865047591932286 chr7 159138663 9659533 0.060698844755281124 0.7794727737398576 chr8 146364022 9164670 0.06261559278550025 0.7661894121982157 chr9 141213431 7362962 0.052140663588862164 0.40617159574811945 chr10 135534747 7891238 0.05822298838245517 0.45114735355171315 chr11 135006516 7825132 0.05796114314956472 0.4470585787987835 chr12 133851895 7656546 0.05720162572222082 0.3281694357800246 chr13 115169878 5479119 0.047574236381495515 0.2720809234195479 chr14 107349540 5518803 0.05140965671580894 1.8318374970334377 chr15 102531392 4598294 0.04484766967759494 0.26580290721835276 chr16 90354753 4229755 0.04681275593769815 0.2933353808337388 chr17 81195210 3881673 0.047806674802614586 0.316707517646712 chr18 78077248 4775002 0.06115740657252674 0.8969667967116262 chr19 59128983 2813358 0.047580016723778255 0.6313222281283846 chr20 63025520 3154345 0.050048694560552616 0.3111366824775426 chr21 48129895 2274217 0.04725165097492941 0.29280153689273425 chr22 51304566 1623514 0.03164462983665041 0.22195746842186936 chrMT 16571 90838 5.481745217548729 4.64033842022153 chrX 155270560 10583325 0.06816053861079653 0.37252198397713876 chrY 59373566 463807 0.007811674980074466 0.12293768324021018