BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094128.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 419,560 number of mapped reads = 376,934 (89.84%) number of supplementary alignments = 5,654 (1.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 189,741 number of mapped paired reads (second in pair) = 187,193 number of mapped paired reads (both in pair) = 372,916 number of mapped paired reads (singletons) = 4,018 number of mapped bases = 53,492,900 bp number of sequenced bases = 53,108,141 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 367,384 duplication rate = 44.57% >>>>>>> Insert size mean insert size = 92,597.9058 std insert size = 2,838,246.118 median insert size = 217 >>>>>>> Mapping quality mean mapping quality = 39.0463 >>>>>>> ACTG content number of A's = 14,516,998 bp (27.33%) number of C's = 11,459,525 bp (21.58%) number of T's = 14,743,573 bp (27.76%) number of G's = 12,387,409 bp (23.32%) number of N's = 636 bp (0%) GC percentage = 44.9% >>>>>>> Mismatches and indels general error rate = 0.0233 number of mismatches = 1,189,978 number of insertions = 23,976 mapped reads with insertion percentage = 6.24% number of deletions = 66,081 mapped reads with deletion percentage = 16.92% homopolymer indels = 46.71% >>>>>>> Coverage mean coverageData = 0.0173X std coverageData = 23.2538X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 229190 9.195162647157456E-4 0.30080382923216503 chr2 243199373 644981 0.002652066870254637 1.6096736354711703 chr3 198022430 2536426 0.012808781308258868 10.067931074279885 chr4 191154276 108174 5.658989286747632E-4 0.2360198917225043 chr5 180915260 79480 4.393217023262714E-4 0.11309143211064253 chr6 171115067 340092 0.0019875047005650298 1.2908594975962455 chr7 159138663 497454 0.0031259154162932737 2.120331258696485 chr8 146364022 1802260 0.012313545196236819 6.014597586795053 chr9 141213431 561208 0.003974182880663809 2.4692235582020334 chr10 135534747 149401 0.0011023077351522263 0.28599770323811513 chr11 135006516 169256 0.0012536876368248774 0.24241312961135575 chr12 133851895 233008 0.0017407896989429996 0.531841642668222 chr13 115169878 250288 0.0021732071297323073 0.6326965019457634 chr14 107349540 29157 2.7160805719335173E-4 0.07328029647022423 chr15 102531392 80085 7.810778575989683E-4 0.19052858369415315 chr16 90354753 56427 6.245050550910145E-4 0.1474005354580003 chr17 81195210 225524 0.002777553010824161 0.5841221799954301 chr18 78077248 48327 6.189639265974129E-4 0.15887882354283878 chr19 59128983 27096 4.5825242757853625E-4 0.1386239144677674 chr20 63025520 43362 6.880070168401625E-4 0.13485348044006018 chr21 48129895 20147 4.1859638380677957E-4 0.0750863056044968 chr22 51304566 235395 0.004588188115654267 2.4126107987370755 chrMT 16571 39579773 2388.49634904351 9654.234241118249 chrX 155270560 5513545 0.03550927490697528 6.591045240958075 chrY 59373566 32844 5.531754653240804E-4 0.17747298147543542