BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708570.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,308,070 number of mapped reads = 3,540,733 (82.19%) number of supplementary alignments = 77 (0%) number of secondary alignments = 0 number of mapped bases = 176,591,170 bp number of sequenced bases = 176,575,599 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,320 duplication rate = 0.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5176 >>>>>>> ACTG content number of A's = 54,695,188 bp (30.98%) number of C's = 33,534,446 bp (18.99%) number of T's = 54,519,017 bp (30.88%) number of G's = 33,822,068 bp (19.15%) number of N's = 4,880 bp (0%) GC percentage = 38.15% >>>>>>> Mismatches and indels general error rate = 0.0016 number of mismatches = 275,512 number of insertions = 11,731 mapped reads with insertion percentage = 0.33% number of deletions = 9,302 mapped reads with deletion percentage = 0.26% homopolymer indels = 47.86% >>>>>>> Coverage mean coverageData = 0.057X std coverageData = 0.246X There is a 5.39% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 13505631 0.05418494423731045 0.24045846495768505 chr2 243199373 16465766 0.06770480448565959 0.26713609811498107 chr3 198022430 13707797 0.0692234561509017 0.26985572915632955 chr4 191154276 14305202 0.07483589851790708 0.28025143805654523 chr5 180915260 11257842 0.06222715540966527 0.2557315928499195 chr6 171115067 11515774 0.06729842206122036 0.26616969473981505 chr7 159138663 9413159 0.05915067289461895 0.25031955962057295 chr8 146364022 9798222 0.06694419752963607 0.26527000332322104 chr9 141213431 7125819 0.05046134032392429 0.2320686195290489 chr10 135534747 7345104 0.054193512457731595 0.23879869923050204 chr11 135006516 7981167 0.05911690217974368 0.25076780495283435 chr12 133851895 7886855 0.05892225134354654 0.24983743413801793 chr13 115169878 6860167 0.059565635729856375 0.25125515601517723 chr14 107349540 5626277 0.05241081610596562 0.2367624610219264 chr15 102531392 4759501 0.04641993936842289 0.22239179627858444 chr16 90354753 3232635 0.03577714389856171 0.19423159749622962 chr17 81195210 2721958 0.03352362781006416 0.18887698943063094 chr18 78077248 4615589 0.059115672212217314 0.24961864180941407 chr19 59128983 1315731 0.022251879420960106 0.15217079543109557 chr20 63025520 2512931 0.039871642471176756 0.2054728245987792 chr21 48129895 2190461 0.04551144356329886 0.22175523906972272 chr22 51304566 1070155 0.020858864686624578 0.14810584195060741 chrMT 16571 499 0.030112847746062398 0.1764572145628567 chrX 155270560 11139039 0.07173954289853789 0.27551498217965875 chrY 59373566 237889 0.004006648345831207 0.06578761639555555