BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548935.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 = 9,778,149 number of mapped reads = 8,517,340 (87.11%) number of secondary alignments = 0 number of mapped bases = 336,892,337 bp number of sequenced bases = 336,855,836 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 344,205 duplication rate = 2.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.2891 >>>>>>> ACTG content number of A's = 98,377,880 bp (29.2%) number of C's = 70,186,385 bp (20.84%) number of T's = 98,689,142 bp (29.3%) number of G's = 69,599,433 bp (20.66%) number of N's = 2,996 bp (0%) GC percentage = 41.5% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 1,036,452 number of insertions = 11,836 mapped reads with insertion percentage = 0.14% number of deletions = 27,823 mapped reads with deletion percentage = 0.33% homopolymer indels = 39.56% >>>>>>> Coverage mean coverageData = 0.1088X std coverageData = 1.4926X There is a 8.76% of reference with a coverageData >= 1X There is a 1.51% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.07% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 27464819 0.11018957100211196 1.550701602115045 chr2 243199373 27293960 0.11222874328709721 0.7374170147657573 chr3 198022430 24007557 0.12123655385907546 0.4167336882399965 chr4 191154276 23215630 0.12144970275213723 0.43198065285087445 chr5 180915260 21810599 0.12055698894609554 0.4291324283278154 chr6 171115067 20249385 0.11833782585609484 0.4807379670590643 chr7 159138663 18534955 0.11647047078685084 1.1785720084726945 chr8 146364022 17553191 0.11992831817644366 5.927584960462795 chr9 141213431 12451677 0.0881762939390659 0.6856306725389835 chr10 135534747 15717940 0.11596981842597161 0.6717075222765191 chr11 135006516 14700719 0.10888895910772188 0.7065526264332234 chr12 133851895 14640443 0.10937792849327983 0.425706582168487 chr13 115169878 11423737 0.09919031953823898 0.36661291606189617 chr14 107349540 10486895 0.09768924021472286 0.45147676922132085 chr15 102531392 9734470 0.09494136195868676 0.36447749350232894 chr16 90354753 9453526 0.10462677043674726 0.4543091145008489 chr17 81195210 8974010 0.11052388435229123 0.44469816847358 chr18 78077248 9262416 0.11863143537026305 1.383673955838469 chr19 59128983 6784818 0.11474606285719476 1.4742834178971522 chr20 63025520 6768453 0.10739225951646254 0.4182020340235665 chr21 48129895 4333470 0.09003697182385292 0.4198214259125035 chr22 51304566 3631798 0.0707889820177019 0.3744371221901386 chrMT 16571 12077 0.7288033311206324 1.1571170773111252 chrX 155270560 17280696 0.1112940920674209 0.5396221453034737 chrY 59373566 1105096 0.018612592681396298 0.23225301549673216