BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082901.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,863,661 number of mapped reads = 1,690,167 (90.69%) number of supplementary alignments = 19,823 (1.06%) number of secondary alignments = 0 number of mapped bases = 112,794,944 bp number of sequenced bases = 112,752,581 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,796 duplication rate = 4.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4766 >>>>>>> ACTG content number of A's = 31,169,161 bp (27.64%) number of C's = 20,753,502 bp (18.41%) number of T's = 36,034,215 bp (31.96%) number of G's = 24,790,347 bp (21.99%) number of N's = 5,356 bp (0%) GC percentage = 40.39% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 790,214 number of insertions = 9,588 mapped reads with insertion percentage = 0.56% number of deletions = 26,139 mapped reads with deletion percentage = 1.53% homopolymer indels = 48.52% >>>>>>> Coverage mean coverageData = 0.0364X std coverageData = 0.3027X There is a 2.97% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 11350716 0.04553936898716894 0.48244033056733593 chr2 243199373 10531081 0.0433022539083602 0.4502713578875924 chr3 198022430 5947834 0.03003616307506175 0.20426805219548833 chr4 191154276 6200901 0.03243924818087773 0.21755136941992678 chr5 180915260 5509818 0.030455241862958383 0.20765267963341033 chr6 171115067 8652469 0.050565208264214394 0.31861749856985017 chr7 159138663 6706806 0.042144415904763505 0.32441327329067277 chr8 146364022 8593253 0.05871151176755719 0.35171612702278404 chr9 141213431 3256492 0.023060780953619065 0.26116576279872394 chr10 135534747 4350530 0.032099001151343134 0.23675136699464996 chr11 135006516 5176668 0.038343838159633714 0.2555706069347279 chr12 133851895 3507529 0.026204552427143448 0.19707722358389745 chr13 115169878 2809680 0.024395962284513316 0.18590252872644336 chr14 107349540 2556170 0.023811653035495074 0.19945312047615205 chr15 102531392 2251418 0.02195832862583198 0.17537634580119837 chr16 90354753 5020233 0.05556136045217234 0.28987686161728443 chr17 81195210 2640488 0.03252024349712255 0.22038996961848376 chr18 78077248 5141514 0.06585162940169202 0.47860663111489454 chr19 59128983 1999295 0.03381243678755645 0.38865760557451196 chr20 63025520 2661061 0.04222196024721415 0.2493828520687247 chr21 48129895 2009844 0.041758744746897954 0.24756005520144184 chr22 51304566 852382 0.016614154771331657 0.15007976502751713 chrMT 16571 134096 8.092209281274515 6.39579638507779 chrX 155270560 4732680 0.03048021466529135 0.21766790745144196 chrY 59373566 201986 0.003401951636187727 0.07412785371032003