BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506011.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 = 8,670,563 number of mapped reads = 3,924,535 (45.26%) number of supplementary alignments = 167 (0%) number of secondary alignments = 0 number of mapped bases = 183,151,864 bp number of sequenced bases = 183,112,940 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 275,270 duplication rate = 5.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.374 >>>>>>> ACTG content number of A's = 54,277,028 bp (29.64%) number of C's = 36,383,315 bp (19.87%) number of T's = 54,573,368 bp (29.8%) number of G's = 37,266,137 bp (20.35%) number of N's = 613,092 bp (0.33%) GC percentage = 40.22% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,469,037 number of insertions = 8,285 mapped reads with insertion percentage = 0.21% number of deletions = 27,739 mapped reads with deletion percentage = 0.7% homopolymer indels = 46.63% >>>>>>> Coverage mean coverageData = 0.0592X std coverageData = 0.5103X There is a 4.43% of reference with a coverageData >= 1X There is a 0.99% of reference with a coverageData >= 2X There is a 0.27% 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 17664919 0.07087211630257081 0.9034286719386068 chr2 243199373 11020679 0.04531540876957771 0.399271521770617 chr3 198022430 11733533 0.05925355526644128 0.3122773361523654 chr4 191154276 7466066 0.039057802714285085 0.259051818970098 chr5 180915260 13412538 0.07413712917307252 0.35403778402552283 chr6 171115067 13082709 0.07645562269510726 0.4827107037569432 chr7 159138663 11167480 0.07017452446486873 0.6241819686346398 chr8 146364022 10698555 0.07309552480048682 0.6731952907970458 chr9 141213431 8608151 0.06095844381827958 0.4239051607223754 chr10 135534747 5693849 0.04201025291322527 0.5378991716131356 chr11 135006516 9306677 0.06893502088447345 0.40168754230205905 chr12 133851895 5061352 0.03781307690862352 0.27720065254607906 chr13 115169878 6161245 0.05349701768373845 0.29504703885704725 chr14 107349540 6278721 0.05848856921045027 0.9116645859194701 chr15 102531392 5990280 0.05842386300578071 0.30787022266271824 chr16 90354753 5590164 0.06186906404359271 0.3643490349663414 chr17 81195210 2635280 0.03245610178235884 0.24946947182941995 chr18 78077248 5869445 0.07517484478961144 0.7416433785136556 chr19 59128983 4130081 0.06984867302723607 0.7339235507626953 chr20 63025520 4496733 0.07134781275902206 0.35523092395607603 chr21 48129895 2512149 0.05219518970486015 0.313523522709772 chr22 51304566 1205488 0.02349670007928729 0.19032781273097443 chrMT 16571 8792 0.5305654456580774 0.9701784397884148 chrX 155270560 12794060 0.08239849202579033 0.41292974439906216 chrY 59373566 562918 0.009480953190515793 0.16790696296895385