BamQC report ----------------------------------- >>>>>>> Input bam file = SRR26104290.sorted.bam outfile = /mainsd2/zhouyj/SRP461548/SRP461548.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 = 44,475,822 number of mapped reads = 42,849,406 (96.34%) number of supplementary alignments = 42,069 (0.09%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 21,715,758 number of mapped paired reads (second in pair) = 21,133,648 number of mapped paired reads (both in pair) = 42,212,052 number of mapped paired reads (singletons) = 637,354 number of mapped bases = 3,195,046,667 bp number of sequenced bases = 3,194,259,449 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,170,559 duplication rate = 40.27% >>>>>>> Insert size mean insert size = 11,265.484 std insert size = 1,036,840.4057 median insert size = 94 >>>>>>> Mapping quality mean mapping quality = 52.8435 >>>>>>> ACTG content number of A's = 815,433,445 bp (25.53%) number of C's = 791,332,738 bp (24.77%) number of T's = 831,983,552 bp (26.05%) number of G's = 753,832,108 bp (23.6%) number of N's = 1,677,606 bp (0.05%) GC percentage = 48.37% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 18,035,643 number of insertions = 293,618 mapped reads with insertion percentage = 0.68% number of deletions = 353,357 mapped reads with deletion percentage = 0.82% homopolymer indels = 46.01% >>>>>>> Coverage mean coverageData = 1.0321X std coverageData = 59.9473X There is a 21.08% of reference with a coverageData >= 1X There is a 11.27% of reference with a coverageData >= 2X There is a 6.18% of reference with a coverageData >= 3X There is a 4.66% of reference with a coverageData >= 4X There is a 3.33% of reference with a coverageData >= 5X There is a 2.79% of reference with a coverageData >= 6X There is a 2.24% of reference with a coverageData >= 7X There is a 1.97% of reference with a coverageData >= 8X There is a 1.68% of reference with a coverageData >= 9X There is a 1.52% of reference with a coverageData >= 10X There is a 1.34% of reference with a coverageData >= 11X There is a 1.23% of reference with a coverageData >= 12X There is a 1.1% of reference with a coverageData >= 13X There is a 1.03% of reference with a coverageData >= 14X There is a 0.94% of reference with a coverageData >= 15X There is a 0.88% of reference with a coverageData >= 16X There is a 0.81% of reference with a coverageData >= 17X There is a 0.77% of reference with a coverageData >= 18X There is a 0.71% of reference with a coverageData >= 19X There is a 0.68% of reference with a coverageData >= 20X There is a 0.64% of reference with a coverageData >= 21X There is a 0.61% of reference with a coverageData >= 22X There is a 0.57% of reference with a coverageData >= 23X There is a 0.55% of reference with a coverageData >= 24X There is a 0.52% of reference with a coverageData >= 25X There is a 0.5% of reference with a coverageData >= 26X There is a 0.47% of reference with a coverageData >= 27X There is a 0.45% of reference with a coverageData >= 28X There is a 0.43% of reference with a coverageData >= 29X There is a 0.42% of reference with a coverageData >= 30X There is a 0.4% of reference with a coverageData >= 31X There is a 0.39% of reference with a coverageData >= 32X There is a 0.37% of reference with a coverageData >= 33X There is a 0.36% of reference with a coverageData >= 34X There is a 0.35% of reference with a coverageData >= 35X There is a 0.33% of reference with a coverageData >= 36X There is a 0.32% of reference with a coverageData >= 37X There is a 0.31% of reference with a coverageData >= 38X There is a 0.3% of reference with a coverageData >= 39X There is a 0.29% of reference with a coverageData >= 40X There is a 0.28% of reference with a coverageData >= 41X There is a 0.27% of reference with a coverageData >= 42X There is a 0.27% of reference with a coverageData >= 43X There is a 0.26% of reference with a coverageData >= 44X There is a 0.25% of reference with a coverageData >= 45X There is a 0.24% of reference with a coverageData >= 46X There is a 0.24% of reference with a coverageData >= 47X There is a 0.23% of reference with a coverageData >= 48X There is a 0.22% of reference with a coverageData >= 49X There is a 0.22% of reference with a coverageData >= 50X There is a 0.21% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 344038684 1.380292183905933 28.332541461224505 chr2 243199373 205863137 0.8464788969665641 7.621097103848981 chr3 198022430 156594924 0.7907938711791387 5.302173698908128 chr4 191154276 128684687 0.6731980560037276 4.236810879510631 chr5 180915260 142688307 0.7887024400263416 8.857788748607314 chr6 171115067 183206862 1.0706647007302987 6.760514714862405 chr7 159138663 182546636 1.1470916781549183 8.06792206020979 chr8 146364022 115206194 0.787120990703576 8.95491987978116 chr9 141213431 104190202 0.737820767204502 6.0802707303134635 chr10 135534747 109138021 0.8052401573450386 5.847498042886015 chr11 135006516 143243009 1.0610081146009278 9.068696409000362 chr12 133851895 120896588 0.9032116280460579 6.286585829671711 chr13 115169878 52708594 0.4576595453196538 10.95657973040998 chr14 107349540 59987484 0.5588052263661307 4.535024830057876 chr15 102531392 79976643 0.7800210398001813 5.503722635083803 chr16 90354753 103077082 1.140804203183423 7.891918445890176 chr17 81195210 109345588 1.3466999839029914 9.625535787439086 chr18 78077248 46966332 0.6015367242451988 4.586219477749793 chr19 59128983 144291496 2.440283743760653 14.317427844497615 chr20 63025520 62305588 0.9885771351033676 6.333939770721471 chr21 48129895 35348741 0.7344445899996249 6.9661081527581565 chr22 51304566 76180622 1.4848702160349627 13.301315492174322 chrMT 16571 412174559 24873.245971878583 5611.311532001685 chrX 155270560 73035475 0.47037554962125466 3.49911463262725 chrY 59373566 3351212 0.05644282844658514 2.378563639219707