BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472677.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 = 14,546,658 number of mapped reads = 14,416,401 (99.1%) number of supplementary alignments = 86,811 (0.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,228,199 number of mapped paired reads (second in pair) = 7,188,202 number of mapped paired reads (both in pair) = 14,326,050 number of mapped paired reads (singletons) = 90,351 number of mapped bases = 1,415,200,432 bp number of sequenced bases = 1,415,000,595 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,751,704 duplication rate = 48.18% >>>>>>> Insert size mean insert size = 20,273.6675 std insert size = 1,394,842.1454 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 54.7825 >>>>>>> ACTG content number of A's = 383,086,689 bp (27.07%) number of C's = 326,787,077 bp (23.09%) number of T's = 382,586,346 bp (27.04%) number of G's = 322,285,762 bp (22.78%) number of N's = 254,721 bp (0.02%) GC percentage = 45.87% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 9,827,272 number of insertions = 92,736 mapped reads with insertion percentage = 0.64% number of deletions = 78,471 mapped reads with deletion percentage = 0.54% homopolymer indels = 46.92% >>>>>>> Coverage mean coverageData = 0.4572X std coverageData = 21.4359X There is a 3.03% of reference with a coverageData >= 1X There is a 1.41% of reference with a coverageData >= 2X There is a 0.68% of reference with a coverageData >= 3X There is a 0.53% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.37% of reference with a coverageData >= 6X There is a 0.34% of reference with a coverageData >= 7X There is a 0.31% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.28% of reference with a coverageData >= 10X There is a 0.27% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.25% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.23% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.21% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.19% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.17% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.16% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.15% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 166693608 0.6687791080769263 26.40649489597492 chr2 243199373 97838250 0.4022964730258577 20.512019955005133 chr3 198022430 122216422 0.6171847401327213 24.014636764566408 chr4 191154276 27148339 0.1420231844565172 6.971404793578266 chr5 180915260 47349428 0.26172158169520915 11.195181379855526 chr6 171115067 96580771 0.5644200285413791 24.399575715277006 chr7 159138663 102588453 0.6446482021782476 25.6103650100024 chr8 146364022 74376073 0.5081581660826456 16.4067685863185 chr9 141213431 96173704 0.6810521019066522 23.674187654569447 chr10 135534747 43267090 0.31923245483315066 15.852334506895849 chr11 135006516 51909229 0.38449424915164837 20.099586209712815 chr12 133851895 54792568 0.4093522022979204 14.857853912820365 chr13 115169878 35590977 0.30903025702606024 12.499320349916788 chr14 107349540 16708999 0.15565040148285683 7.159038815250079 chr15 102531392 13962168 0.13617456788258567 8.003647787720801 chr16 90354753 91924970 1.017378355292499 54.67510944512097 chr17 81195210 49079175 0.6044589945638419 20.066088356298334 chr18 78077248 6698333 0.08579110011664345 3.591690804826114 chr19 59128983 34718630 0.5871677177332815 17.048566925993534 chr20 63025520 63404721 1.0060166262809096 31.769649743358023 chr21 48129895 11624467 0.2415227999146892 21.988751060747614 chr22 51304566 23030744 0.4489024232268138 23.659827401754274 chrMT 16571 2182 0.13167581920222074 0.4234028951444773 chrX 155270560 86841794 0.5592933650783509 24.129653744756617 chrY 59373566 679337 0.011441741599283425 0.45807369181785407