BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506322.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 4,376,677 number of mapped reads = 3,104,668 (70.94%) number of supplementary alignments = 42,703 (0.98%) number of secondary alignments = 0 number of mapped bases = 246,165,938 bp number of sequenced bases = 246,063,666 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 372,965 duplication rate = 9.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6579 >>>>>>> ACTG content number of A's = 65,836,403 bp (26.76%) number of C's = 47,589,970 bp (19.34%) number of T's = 70,785,567 bp (28.77%) number of G's = 61,793,794 bp (25.11%) number of N's = 57,932 bp (0.02%) GC percentage = 44.45% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 1,671,390 number of insertions = 19,782 mapped reads with insertion percentage = 0.62% number of deletions = 49,228 mapped reads with deletion percentage = 1.55% homopolymer indels = 42.26% >>>>>>> Coverage mean coverageData = 0.0795X std coverageData = 0.58X There is a 5.36% of reference with a coverageData >= 1X There is a 1.54% of reference with a coverageData >= 2X There is a 0.53% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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% 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 19298932 0.07742781912667732 0.9708695277866964 chr2 243199373 20658444 0.08494447886590563 0.6442816865710016 chr3 198022430 16068972 0.0811472316545151 0.39490336065175385 chr4 191154276 14246560 0.07452912013331055 0.5360727894208641 chr5 180915260 20292794 0.11216739815093542 0.4746454740180515 chr6 171115067 7260622 0.042431225533167104 0.3006056288127993 chr7 159138663 14622030 0.09188232277658384 0.781191459155301 chr8 146364022 13866965 0.09474298950325374 0.6132564698884065 chr9 141213431 6105827 0.043238288006754826 0.47789106543212384 chr10 135534747 14317452 0.1056367633902766 0.709873122005199 chr11 135006516 9591744 0.07104652637654911 0.4801202995934242 chr12 133851895 9321049 0.06963703427583151 0.37931393643545686 chr13 115169878 4955463 0.04302742250017839 0.282399935245882 chr14 107349540 7479704 0.069676162562038 0.38348593887712107 chr15 102531392 8789439 0.08572437015192381 0.4184291436691253 chr16 90354753 8880578 0.09828567623885819 0.5128794816106994 chr17 81195210 6872841 0.08464589228847366 0.48768188056082745 chr18 78077248 4927301 0.06310802604108177 0.7177737743591535 chr19 59128983 6892008 0.11655887942466388 0.7692912849913441 chr20 63025520 6468968 0.10264045421600647 0.488939354628033 chr21 48129895 4161711 0.08646831662524923 0.5152576324584192 chr22 51304566 2628235 0.05122809147240423 0.34188472153831345 chrMT 16571 44339 2.6756985094442096 2.6415426839138867 chrX 155270560 17468010 0.11250046370670654 0.5142975262847278 chrY 59373566 945950 0.015932174260848676 0.6133030718568292