BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472583.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 10,266,670 number of mapped reads = 9,369,521 (91.26%) number of supplementary alignments = 286,326 (2.79%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,724,488 number of mapped paired reads (second in pair) = 4,645,033 number of mapped paired reads (both in pair) = 9,154,932 number of mapped paired reads (singletons) = 214,589 number of mapped bases = 756,825,033 bp number of sequenced bases = 756,503,197 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,597,882 duplication rate = 14.72% >>>>>>> Insert size mean insert size = 217,045.6118 std insert size = 4,492,447.9287 median insert size = 126 >>>>>>> Mapping quality mean mapping quality = 50.4895 >>>>>>> ACTG content number of A's = 195,155,907 bp (25.8%) number of C's = 151,419,616 bp (20.02%) number of T's = 224,935,583 bp (29.73%) number of G's = 184,488,479 bp (24.39%) number of N's = 503,612 bp (0.07%) GC percentage = 44.4% >>>>>>> Mismatches and indels general error rate = 0.0121 number of mismatches = 9,023,889 number of insertions = 71,969 mapped reads with insertion percentage = 0.75% number of deletions = 171,939 mapped reads with deletion percentage = 1.8% homopolymer indels = 42.56% >>>>>>> Coverage mean coverageData = 0.2445X std coverageData = 2.3737X There is a 12.96% of reference with a coverageData >= 1X There is a 6.13% of reference with a coverageData >= 2X There is a 2.26% of reference with a coverageData >= 3X There is a 1.12% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.29% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 50634039 0.2031450866475474 3.5265480474605897 chr2 243199373 75101160 0.3088049079797586 2.7499542611011827 chr3 198022430 40040487 0.2022017758291321 0.6931462027214996 chr4 191154276 39425964 0.20625206417040862 1.3519328270066286 chr5 180915260 36697713 0.20284476279115427 0.748761028784722 chr6 171115067 52869453 0.30897017969785207 1.3911194236178759 chr7 159138663 50739716 0.31883965243568746 3.7124319111601904 chr8 146364022 38995484 0.26642807069076035 2.0954170408096653 chr9 141213431 26877796 0.1903345581908565 2.553691904458676 chr10 135534747 30066184 0.22183377078941977 2.4382584198637605 chr11 135006516 27704678 0.20520993223764103 1.7574035539238768 chr12 133851895 40070575 0.2993650183286535 0.8912174376411085 chr13 115169878 37225748 0.3232246890111319 0.9313988075384662 chr14 107349540 20507745 0.19103710178916464 5.608485864628992 chr15 102531392 18721970 0.1825974429372811 0.66853805899232 chr16 90354753 28518583 0.31562902949886873 1.3611080710889747 chr17 81195210 29424405 0.36239089719701445 2.041575689214891 chr18 78077248 17304276 0.221630198851271 4.6176542868978245 chr19 59128983 16459943 0.27837351777215585 2.433821688252605 chr20 63025520 21839287 0.3465149831369896 1.470634855941046 chr21 48129895 12140506 0.25224459766637763 1.0512495374965334 chr22 51304566 8610817 0.16783724473958128 0.6564166051015872 chrMT 16571 25165 1.5186168607808823 4.641093592625041 chrX 155270560 35009834 0.22547631695280806 1.1315039533978826 chrY 59373566 1813505 0.030543979790602437 1.1183390265465032