BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617380.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 = 32,000,000 number of mapped reads = 30,455,807 (95.17%) number of supplementary alignments = 66,615 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,292,153 number of mapped paired reads (second in pair) = 15,163,654 number of mapped paired reads (both in pair) = 30,021,544 number of mapped paired reads (singletons) = 434,263 number of mapped bases = 2,992,655,937 bp number of sequenced bases = 2,991,780,485 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,579,286 duplication rate = 1.48% >>>>>>> Insert size mean insert size = 52,498.9394 std insert size = 2,200,635.7044 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 53.4946 >>>>>>> ACTG content number of A's = 906,020,859 bp (30.28%) number of C's = 593,839,181 bp (19.85%) number of T's = 893,882,523 bp (29.88%) number of G's = 596,583,014 bp (19.94%) number of N's = 1,454,908 bp (0.05%) GC percentage = 39.79% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 31,688,813 number of insertions = 299,511 mapped reads with insertion percentage = 0.95% number of deletions = 363,489 mapped reads with deletion percentage = 1.16% homopolymer indels = 41.22% >>>>>>> Coverage mean coverageData = 0.9667X std coverageData = 9.8838X There is a 53.34% of reference with a coverageData >= 1X There is a 24.24% of reference with a coverageData >= 2X There is a 9.38% of reference with a coverageData >= 3X There is a 3.31% of reference with a coverageData >= 4X There is a 1.14% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 194046060 0.778517859740859 20.00936585640451 chr2 243199373 295720598 1.215959541145692 8.97084414291552 chr3 198022430 238166645 1.2027255952772622 1.4941993141678978 chr4 191154276 164140736 0.8586819998732332 9.562223217945638 chr5 180915260 187788329 1.0379905431968537 1.4755316888801033 chr6 171115067 140435371 0.8207072203641775 3.673545838805949 chr7 159138663 242965300 1.526752175868161 10.944176185597968 chr8 146364022 126105559 0.861588505677987 7.715533350694105 chr9 141213431 126031747 0.8924912177794193 14.982543393884303 chr10 135534747 126022682 0.9298182553880445 20.469055655317547 chr11 135006516 160600326 1.1895746276424168 5.596380961442595 chr12 133851895 131926661 0.9856166847693864 1.3395932448455525 chr13 115169878 130452229 1.132693993129002 1.299305584041205 chr14 107349540 86741974 0.8080330292984954 1.3672703552964451 chr15 102531392 67153361 0.6549541529680978 0.9791824770103524 chr16 90354753 75006934 0.8301382219483241 7.942816398138444 chr17 81195210 92740533 1.142192168725224 7.219863494858124 chr18 78077248 54122438 0.6931909024252494 15.366981167175016 chr19 59128983 55462871 0.9379980541860495 9.84841837175584 chr20 63025520 85867924 1.3624310279391587 2.51391251098779 chr21 48129895 47748054 0.9920664485139641 3.2562702015359926 chr22 51304566 26437503 0.5153050705077595 0.9172704913161662 chrMT 16571 2060862 124.36557842013156 22.870436671733454 chrX 155270560 124725904 0.8032810856095322 3.0688572782910057 chrY 59373566 10185336 0.17154664417495152 8.44654328536928