BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013168.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,749,351 number of mapped reads = 1,494,506 (85.43%) number of supplementary alignments = 15,472 (0.88%) number of secondary alignments = 0 number of mapped bases = 99,257,406 bp number of sequenced bases = 99,209,717 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,857 duplication rate = 4.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.421 >>>>>>> ACTG content number of A's = 27,427,853 bp (27.65%) number of C's = 18,396,669 bp (18.54%) number of T's = 31,469,879 bp (31.72%) number of G's = 21,913,862 bp (22.09%) number of N's = 1,454 bp (0%) GC percentage = 40.63% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 724,642 number of insertions = 7,063 mapped reads with insertion percentage = 0.47% number of deletions = 27,952 mapped reads with deletion percentage = 1.85% homopolymer indels = 46.65% >>>>>>> Coverage mean coverageData = 0.0321X std coverageData = 0.3101X There is a 2.43% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 3644258 0.014620858256557763 0.23419035325786083 chr2 243199373 6660902 0.027388647913989483 0.34564093709511784 chr3 198022430 9122423 0.04606762476351795 0.273021487540443 chr4 191154276 9610037 0.05027372236234987 0.28562755158307157 chr5 180915260 4579743 0.025314299081238365 0.19919971455738283 chr6 171115067 4308884 0.02518120745030594 0.2649324442585283 chr7 159138663 6973425 0.04381980386501048 0.5766192996226229 chr8 146364022 5739167 0.03921159668596699 0.48905463853924946 chr9 141213431 1360682 0.009635641527610784 0.24573161199509624 chr10 135534747 7750182 0.05718225157420333 0.38698241993063814 chr11 135006516 5079599 0.03762484323349252 0.31410972916169166 chr12 133851895 4245983 0.03172150084240496 0.2299086709202519 chr13 115169878 499551 0.004337514362913539 0.08085168893153406 chr14 107349540 4461828 0.041563550249027616 0.26778367580745266 chr15 102531392 3412698 0.033284420833767675 0.2295662205983446 chr16 90354753 3733471 0.04132013951717626 0.2639267253594608 chr17 81195210 3353439 0.041300946201136744 0.28656549982512386 chr18 78077248 4111554 0.052660078388008756 0.517192272955476 chr19 59128983 1098151 0.018572127310222807 0.2554228452533623 chr20 63025520 3618972 0.05742074004308096 0.30772625874410736 chr21 48129895 1640231 0.03407925573076775 0.23558025267311375 chr22 51304566 1168449 0.022774756539213292 0.18710172464454042 chrMT 16571 46175 2.7864944783054733 2.6557056527662435 chrX 155270560 2872174 0.018497865918690574 0.18262519667477484 chrY 59373566 165428 0.002786223081160394 0.06346465385183184