BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082677.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 = 3,387,762 number of mapped reads = 3,118,008 (92.04%) number of supplementary alignments = 14,185 (0.42%) number of secondary alignments = 0 number of mapped bases = 206,287,321 bp number of sequenced bases = 206,207,711 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 137,955 duplication rate = 3.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7464 >>>>>>> ACTG content number of A's = 56,648,724 bp (27.47%) number of C's = 35,301,587 bp (17.12%) number of T's = 68,769,220 bp (33.35%) number of G's = 45,432,711 bp (22.03%) number of N's = 55,469 bp (0.03%) GC percentage = 39.15% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,894,642 number of insertions = 18,632 mapped reads with insertion percentage = 0.59% number of deletions = 49,153 mapped reads with deletion percentage = 1.56% homopolymer indels = 49.05% >>>>>>> Coverage mean coverageData = 0.0666X std coverageData = 0.5584X There is a 5.44% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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% 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 19938533 0.07999391504023574 0.7743309055716917 chr2 243199373 20581169 0.08462673544803917 0.9070218564670366 chr3 198022430 14825587 0.0748682207364085 0.32336888120244334 chr4 191154276 11887769 0.062189396171289414 0.29951861014663317 chr5 180915260 10592903 0.058551738532172465 0.28341520558675504 chr6 171115067 14778272 0.08636452802838221 0.6833853171471154 chr7 159138663 10386826 0.06526902893484784 0.600707498249895 chr8 146364022 19204535 0.1312107629838158 0.7191952966887462 chr9 141213431 5574053 0.03947254139020247 0.6269487465787063 chr10 135534747 7303789 0.0538886828777568 0.42936556074192694 chr11 135006516 7626603 0.05649062894119866 0.44813793758118614 chr12 133851895 6360676 0.04752025363555742 0.26946070926567994 chr13 115169878 4826489 0.04190756371210187 0.23364135261081262 chr14 107349540 4471430 0.04165299637054803 0.33436442920435006 chr15 102531392 2629989 0.025650573436084824 0.18492051619029687 chr16 90354753 7709423 0.08532393420410324 0.383432561524569 chr17 81195210 3998634 0.04924716618135479 0.3980822362519082 chr18 78077248 10905388 0.13967433893161807 1.2298101348674344 chr19 59128983 2782704 0.04706159075998314 0.6521132845265585 chr20 63025520 3631007 0.057611694437427884 0.31138129701586914 chr21 48129895 4683190 0.09730314184146881 0.38266032255199106 chr22 51304566 2233182 0.04352793862441016 0.24039126588957085 chrMT 16571 5089 0.30710276989922153 0.6139485603128395 chrX 155270560 8994801 0.05792985482888707 0.38326855123545644 chrY 59373566 355280 0.005983807676298237 0.12326295494348777