BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708514.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 = 3,218,636 number of mapped reads = 2,231,771 (69.34%) number of supplementary alignments = 474 (0.01%) number of secondary alignments = 0 number of mapped bases = 107,141,471 bp number of sequenced bases = 107,120,661 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 114,417 duplication rate = 3.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0552 >>>>>>> ACTG content number of A's = 31,088,211 bp (29.02%) number of C's = 19,769,779 bp (18.46%) number of T's = 34,427,368 bp (32.14%) number of G's = 21,833,884 bp (20.38%) number of N's = 1,419 bp (0%) GC percentage = 38.84% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 541,599 number of insertions = 5,369 mapped reads with insertion percentage = 0.24% number of deletions = 13,807 mapped reads with deletion percentage = 0.62% homopolymer indels = 47.99% >>>>>>> Coverage mean coverageData = 0.0346X std coverageData = 0.3617X There is a 2.88% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 8408314 0.033734375329801086 0.6299383294680482 chr2 243199373 9365934 0.03851134106336697 0.38120212264910536 chr3 198022430 7741615 0.03909463690552631 0.23345334163265233 chr4 191154276 7403339 0.03872965415641552 0.23446369298712405 chr5 180915260 6691723 0.0369881623031689 0.22847466761760032 chr6 171115067 6579688 0.038451833116484126 0.27756766306750613 chr7 159138663 6131159 0.038527149119004477 0.397940556645815 chr8 146364022 5708506 0.03900211214474552 0.7970771991608165 chr9 141213431 4733762 0.033522037999345826 0.2527959382588596 chr10 135534747 5073449 0.0374328289409062 0.2815271189432946 chr11 135006516 4812918 0.03564952376076426 0.3181749402883699 chr12 133851895 5000311 0.03735704302131845 0.23104221947028736 chr13 115169878 3778512 0.0328081618702418 0.22275910740774812 chr14 107349540 3320975 0.030936089712168307 0.21346045807326094 chr15 102531392 3001433 0.029273307827518816 0.199976174257323 chr16 90354753 2837622 0.031405342893251004 0.21742846393114076 chr17 81195210 2694700 0.03318791835134117 0.2616583249963258 chr18 78077248 3097765 0.0396756427685566 0.41777637563843134 chr19 59128983 1826116 0.03088360237821104 0.45821367099114263 chr20 63025520 2096719 0.03326777787791358 0.21791820200931883 chr21 48129895 1499044 0.0311457982611431 0.2517631097210633 chr22 51304566 1066697 0.02079146327833667 0.19207868017810845 chrMT 16571 141997 8.569006094985214 5.986480602930626 chrX 155270560 3433749 0.022114617220418346 0.20477430005716035 chrY 59373566 695424 0.011712687090413267 0.1326612582783064