BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618274.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 741,419,584 number of mapped reads = 691,077,122 (93.21%) number of supplementary alignments = 9,020,488 (1.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 347,935,873 number of mapped paired reads (second in pair) = 343,141,249 number of mapped paired reads (both in pair) = 670,989,710 number of mapped paired reads (singletons) = 20,087,412 number of mapped bases = 61,062,611,019 bp number of sequenced bases = 61,027,641,615 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 326,082,966 duplication rate = 27.03% >>>>>>> Insert size mean insert size = 184,720.5805 std insert size = 4,130,291.0365 median insert size = 185 >>>>>>> Mapping quality mean mapping quality = 51.4829 >>>>>>> ACTG content number of A's = 17,720,704,858 bp (29.04%) number of C's = 11,373,010,581 bp (18.64%) number of T's = 18,264,992,948 bp (29.93%) number of G's = 13,647,092,974 bp (22.36%) number of N's = 21,840,254 bp (0.04%) GC percentage = 41% >>>>>>> Mismatches and indels general error rate = 0.0126 number of mismatches = 753,680,348 number of insertions = 8,983,498 mapped reads with insertion percentage = 1.27% number of deletions = 20,966,954 mapped reads with deletion percentage = 2.97% homopolymer indels = 47.11% >>>>>>> Coverage mean coverageData = 19.725X std coverageData = 240.6525X There is a 72.29% of reference with a coverageData >= 1X There is a 66.73% of reference with a coverageData >= 2X There is a 62.4% of reference with a coverageData >= 3X There is a 58.77% of reference with a coverageData >= 4X There is a 55.56% of reference with a coverageData >= 5X There is a 52.67% of reference with a coverageData >= 6X There is a 50.04% of reference with a coverageData >= 7X There is a 47.61% of reference with a coverageData >= 8X There is a 45.37% of reference with a coverageData >= 9X There is a 43.29% of reference with a coverageData >= 10X There is a 41.35% of reference with a coverageData >= 11X There is a 39.53% of reference with a coverageData >= 12X There is a 37.83% of reference with a coverageData >= 13X There is a 36.23% of reference with a coverageData >= 14X There is a 34.72% of reference with a coverageData >= 15X There is a 33.3% of reference with a coverageData >= 16X There is a 31.96% of reference with a coverageData >= 17X There is a 30.69% of reference with a coverageData >= 18X There is a 29.49% of reference with a coverageData >= 19X There is a 28.35% of reference with a coverageData >= 20X There is a 27.27% of reference with a coverageData >= 21X There is a 26.24% of reference with a coverageData >= 22X There is a 25.26% of reference with a coverageData >= 23X There is a 24.33% of reference with a coverageData >= 24X There is a 23.45% of reference with a coverageData >= 25X There is a 22.6% of reference with a coverageData >= 26X There is a 21.8% of reference with a coverageData >= 27X There is a 21.03% of reference with a coverageData >= 28X There is a 20.29% of reference with a coverageData >= 29X There is a 19.59% of reference with a coverageData >= 30X There is a 18.92% of reference with a coverageData >= 31X There is a 18.28% of reference with a coverageData >= 32X There is a 17.67% of reference with a coverageData >= 33X There is a 17.08% of reference with a coverageData >= 34X There is a 16.52% of reference with a coverageData >= 35X There is a 15.98% of reference with a coverageData >= 36X There is a 15.46% of reference with a coverageData >= 37X There is a 14.97% of reference with a coverageData >= 38X There is a 14.49% of reference with a coverageData >= 39X There is a 14.03% of reference with a coverageData >= 40X There is a 13.59% of reference with a coverageData >= 41X There is a 13.17% of reference with a coverageData >= 42X There is a 12.77% of reference with a coverageData >= 43X There is a 12.38% of reference with a coverageData >= 44X There is a 12.01% of reference with a coverageData >= 45X There is a 11.65% of reference with a coverageData >= 46X There is a 11.3% of reference with a coverageData >= 47X There is a 10.97% of reference with a coverageData >= 48X There is a 10.64% of reference with a coverageData >= 49X There is a 10.33% of reference with a coverageData >= 50X There is a 10.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4064067672 16.305145622886933 279.2601889175376 chr2 243199373 6368336480 26.185661588856153 366.1591859362739 chr3 198022430 4993492059 25.216800233185705 41.92182458535253 chr4 191154276 3080214636 16.11376266571196 131.62977412531288 chr5 180915260 3854231320 21.304069761721593 42.53042239058348 chr6 171115067 2928278672 17.112921283547756 139.84131213605468 chr7 159138663 4740383359 29.787754085881694 354.0762185759148 chr8 146364022 2724201008 18.612504430904476 120.32331292269623 chr9 141213431 2548436391 18.046699757617247 508.1497524003239 chr10 135534747 2566356645 18.935045822603705 302.42199222523743 chr11 135006516 3366157088 24.933293501181826 245.20584150742653 chr12 133851895 2698393554 20.15954689322852 42.63144695095419 chr13 115169878 2525696237 21.930180710966802 38.71017106966811 chr14 107349540 1798511467 16.753788297555815 78.40320395750923 chr15 102531392 1427678882 13.924309951824316 28.942988242479892 chr16 90354753 1524232831 16.869426127477766 197.39782517375275 chr17 81195210 1762792571 21.710548824247144 326.4787502080143 chr18 78077248 1149270164 14.719655129238161 502.6373421213359 chr19 59128983 797531827 13.488001763872719 173.95266980034262 chr20 63025520 1815221923 28.80137955228295 58.95793105360271 chr21 48129895 846731243 17.592626017571824 78.19084822132977 chr22 51304566 469265271 9.146657063622758 26.95830185776869 chrMT 16571 88615243 5347.609860599843 3072.105472726481 chrX 155270560 2732457103 17.598037277639754 112.90700709392783 chrY 59373566 192057373 3.234728616435132 215.90190792031353