BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549138.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 13,062,297 number of mapped reads = 11,191,859 (85.68%) number of secondary alignments = 0 number of mapped bases = 443,788,217 bp number of sequenced bases = 443,745,990 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 819,656 duplication rate = 5.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7312 >>>>>>> ACTG content number of A's = 129,008,332 bp (29.07%) number of C's = 91,599,327 bp (20.64%) number of T's = 130,839,574 bp (29.49%) number of G's = 92,200,528 bp (20.78%) number of N's = 98,229 bp (0.02%) GC percentage = 41.42% >>>>>>> Mismatches and indels general error rate = 0.0033 number of mismatches = 1,436,754 number of insertions = 11,657 mapped reads with insertion percentage = 0.1% number of deletions = 33,485 mapped reads with deletion percentage = 0.3% homopolymer indels = 44.53% >>>>>>> Coverage mean coverageData = 0.1434X std coverageData = 1.0579X There is a 8.85% of reference with a coverageData >= 1X There is a 3.19% of reference with a coverageData >= 2X There is a 1.22% of reference with a coverageData >= 3X There is a 0.48% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 36867781 0.14791450008062368 1.7476484921394038 chr2 243199373 37807827 0.15546021576297403 0.840268725660543 chr3 198022430 30298529 0.15300554083696477 0.5770820928001378 chr4 191154276 29002802 0.1517245787376475 0.6850761201062818 chr5 180915260 27727035 0.15325979135203963 0.5900593270438298 chr6 171115067 26156691 0.15286024462124076 0.6250583160168717 chr7 159138663 24580163 0.1544575185981046 1.1880527117503006 chr8 146364022 22935053 0.15669870700874836 2.7339956520554023 chr9 141213431 18905393 0.13387815072632858 0.7422297074708216 chr10 135534747 21198164 0.15640390725781927 0.9523482522107551 chr11 135006516 20752912 0.15371785462562415 0.7342126429929045 chr12 133851895 20786303 0.1552933038415332 0.6058670788846038 chr13 115169878 14182570 0.12314478617403762 0.5144940981739976 chr14 107349540 13674782 0.12738556681286198 0.6946094241144868 chr15 102531392 13144658 0.12820130248499895 0.5219788302101513 chr16 90354753 12638801 0.13987975817940645 0.6093781247081551 chr17 81195210 12303551 0.15153050284616543 0.6143154589632107 chr18 78077248 11623894 0.14887684053618283 1.4849575146840757 chr19 59128983 9139447 0.1545679721905584 1.3987329819546075 chr20 63025520 9519929 0.15104879737604704 0.6357546287594961 chr21 48129895 5790349 0.12030670334934244 0.6545698141976081 chr22 51304566 5356641 0.1044086602350364 0.4904476754741747 chrMT 16571 137366 8.28954197091304 9.51957962053802 chrX 155270560 15175486 0.09773575879419769 0.5555499703796439 chrY 59373566 4082090 0.06875264995873753 0.7378968645454546