BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094015.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 = 27,496 number of mapped reads = 12,642 (45.98%) number of supplementary alignments = 36 (0.13%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,269 number of mapped paired reads (second in pair) = 6,373 number of mapped paired reads (both in pair) = 12,388 number of mapped paired reads (singletons) = 254 number of mapped bases = 1,850,952 bp number of sequenced bases = 1,847,411 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,049 duplication rate = 29.41% >>>>>>> Insert size mean insert size = 30,614.9433 std insert size = 1,398,690.1575 median insert size = 217 >>>>>>> Mapping quality mean mapping quality = 12.3878 >>>>>>> ACTG content number of A's = 550,421 bp (29.79%) number of C's = 360,325 bp (19.5%) number of T's = 542,890 bp (29.39%) number of G's = 393,768 bp (21.31%) number of N's = 7 bp (0%) GC percentage = 40.82% >>>>>>> Mismatches and indels general error rate = 0.0121 number of mismatches = 21,851 number of insertions = 120 mapped reads with insertion percentage = 0.89% number of deletions = 809 mapped reads with deletion percentage = 5.88% homopolymer indels = 37.14% >>>>>>> Coverage mean coverageData = 0.0006X std coverageData = 1.8864X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 11068 4.440510501275742E-5 0.044232195120451526 chr2 243199373 29381 1.208103443589059E-4 0.10943394999999474 chr3 198022430 1955 9.872618975537266E-6 0.005551544640416382 chr4 191154276 1849 9.672815270949E-6 0.003905044347210812 chr5 180915260 1358 7.506276695509268E-6 0.0036588840480556314 chr6 171115067 886 5.177802373183187E-6 0.002999960934718855 chr7 159138663 4031 2.5330111011426556E-5 0.015003081080241017 chr8 146364022 1544 1.0549040528552843E-5 0.004937354351019653 chr9 141213431 1203 8.5190196957965E-6 0.003648713635932142 chr10 135534747 2942 2.1706610777825115E-5 0.012580204368755829 chr11 135006516 470 3.481313450085624E-6 0.0024884297504899127 chr12 133851895 2766 2.0664630859353916E-5 0.009445110680384934 chr13 115169878 1578 1.3701499275704711E-5 0.00559864481582823 chr14 107349540 2785 2.5943287693640794E-5 0.021970713336040105 chr15 102531392 471 4.593715064358045E-6 0.0026991762910937426 chr16 90354753 674 7.459485833578672E-6 0.0033730295923715776 chr17 81195210 6943 8.550997035416251E-5 0.039928207184938565 chr18 78077248 731 9.362522613501951E-6 0.005376539936202431 chr19 59128983 142 2.401529551083265E-6 0.0015496850595327686 chr20 63025520 1113 1.7659513162287276E-5 0.006613915106565577 chr21 48129895 38 7.895300831219349E-7 8.885547027415829E-4 chr22 51304566 375 7.309290950828821E-6 0.0031590450198440236 chrMT 16571 1733451 104.60750709070062 808.4662633991494 chrX 155270560 43136 2.778118401839988E-4 0.05383459360220656 chrY 59373566 62 1.0442357462578548E-6 0.0010218780043770202