BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549063.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 9,826,109 number of mapped reads = 8,464,213 (86.14%) number of secondary alignments = 0 number of mapped bases = 336,555,561 bp number of sequenced bases = 336,522,948 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 468,165 duplication rate = 4.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.581 >>>>>>> ACTG content number of A's = 96,763,245 bp (28.75%) number of C's = 71,383,203 bp (21.21%) number of T's = 97,088,952 bp (28.85%) number of G's = 71,281,338 bp (21.18%) number of N's = 6,210 bp (0%) GC percentage = 42.39% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 1,019,502 number of insertions = 7,694 mapped reads with insertion percentage = 0.09% number of deletions = 25,696 mapped reads with deletion percentage = 0.3% homopolymer indels = 44.56% >>>>>>> Coverage mean coverageData = 0.1087X std coverageData = 1.1746X There is a 7.78% of reference with a coverageData >= 1X There is a 2.05% of reference with a coverageData >= 2X There is a 0.58% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 28124651 0.11283683421595166 2.2639454033907658 chr2 243199373 28541389 0.1173579875964565 0.6651500911825456 chr3 198022430 22714464 0.11470652087240824 0.44434320397365606 chr4 191154276 21468416 0.11230936837635795 0.5409087098634447 chr5 180915260 20686529 0.11434374855940842 0.45546533817998985 chr6 171115067 19469598 0.11378073445747475 0.47743262937552117 chr7 159138663 18838211 0.11837607935665515 0.8738559618465346 chr8 146364022 17942828 0.12259042731143313 3.636809541197682 chr9 141213431 14439471 0.10225281616449075 0.5859681920505285 chr10 135534747 16427433 0.1212045867470428 0.7882770309941148 chr11 135006516 15800233 0.11703311416465262 0.6255907909759231 chr12 133851895 15502644 0.11581938380476421 0.4598007591496115 chr13 115169878 10696181 0.09287307745520057 0.3907368133887588 chr14 107349540 10433414 0.09719104525273234 0.4560859906683698 chr15 102531392 10171897 0.0992076358428841 0.40582436167134117 chr16 90354753 9915460 0.10973921869943024 0.49834398361669163 chr17 81195210 9343142 0.11507011312613145 0.48445740689631656 chr18 78077248 8924311 0.11430104452452013 1.1711771302153713 chr19 59128983 6841716 0.11570833207126191 1.5186509279215232 chr20 63025520 7645806 0.12131285866423633 0.48870506610835307 chr21 48129895 4446009 0.09237520671923344 0.5138343565419154 chr22 51304566 4287480 0.08356917004229214 0.40267056103588394 chrMT 16571 10871 0.6560255868686259 1.1995908306979517 chrX 155270560 10338954 0.06658669872769184 0.4245964213444663 chrY 59373566 3544453 0.059697492315014394 0.7867605470839676