BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004089.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 418,886 number of mapped reads = 337,367 (80.54%) number of supplementary alignments = 2,570 (0.61%) number of secondary alignments = 0 number of mapped bases = 22,486,311 bp number of sequenced bases = 22,473,933 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,600 duplication rate = 1.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3515 >>>>>>> ACTG content number of A's = 6,559,250 bp (29.19%) number of C's = 3,919,750 bp (17.44%) number of T's = 6,971,532 bp (31.02%) number of G's = 5,019,066 bp (22.33%) number of N's = 4,335 bp (0.02%) GC percentage = 39.77% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 233,234 number of insertions = 2,057 mapped reads with insertion percentage = 0.6% number of deletions = 7,369 mapped reads with deletion percentage = 2.15% homopolymer indels = 44.59% >>>>>>> Coverage mean coverageData = 0.0073X std coverageData = 0.0995X There is a 0.7% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 1674364 0.0067175920897705604 0.12771922985490905 chr2 243199373 1891097 0.007775912317010784 0.10548882766741122 chr3 198022430 985170 0.00497504247372381 0.07191056068701654 chr4 191154276 1760764 0.009211219528251621 0.09809142576251201 chr5 180915260 1400148 0.007739247645555162 0.09018066905774971 chr6 171115067 1711562 0.010002403821049844 0.10506966867215384 chr7 159138663 1680473 0.010559803433814196 0.11897962023352812 chr8 146364022 1548324 0.010578583307856899 0.14969007852796706 chr9 141213431 793714 0.0056206693257102435 0.0891195761117844 chr10 135534747 893878 0.006595194367389788 0.08830160009844752 chr11 135006516 1083691 0.00802695330646115 0.09987385198099608 chr12 133851895 1177331 0.008795773866331888 0.0962067783155254 chr13 115169878 596880 0.005182605125274162 0.07336475292966449 chr14 107349540 525016 0.004890714948568946 0.07278807895754436 chr15 102531392 490498 0.004783881213667712 0.07065191509425191 chr16 90354753 593124 0.006564391803494831 0.08496299683789568 chr17 81195210 509330 0.006272906985522914 0.08160711556566677 chr18 78077248 721120 0.00923598126819224 0.14158976109090216 chr19 59128983 272522 0.0046089411008472785 0.09206586619878857 chr20 63025520 558178 0.008856380716890554 0.09768537730148756 chr21 48129895 297081 0.0061724838585249355 0.08121455752111949 chr22 51304566 140873 0.0027458179843096227 0.053077000062940624 chrMT 16571 2689 0.16227143805443245 0.40270202499565516 chrX 155270560 1133398 0.0072995035246862 0.08941928664470888 chrY 59373566 45086 7.593614976738975E-4 0.02920246261420178