BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124824.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 24,807,268 number of mapped reads = 24,462,848 (98.61%) number of supplementary alignments = 217,857 (0.88%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,252,722 number of mapped paired reads (second in pair) = 12,210,126 number of mapped paired reads (both in pair) = 24,369,736 number of mapped paired reads (singletons) = 93,112 number of mapped bases = 2,102,757,616 bp number of sequenced bases = 2,101,704,600 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,677,712 duplication rate = 12.63% >>>>>>> Insert size mean insert size = 96,428.4327 std insert size = 2,946,496.3475 median insert size = 185 >>>>>>> Mapping quality mean mapping quality = 52.5331 >>>>>>> ACTG content number of A's = 599,759,418 bp (28.54%) number of C's = 387,098,952 bp (18.42%) number of T's = 632,515,473 bp (30.1%) number of G's = 482,312,678 bp (22.95%) number of N's = 18,079 bp (0%) GC percentage = 41.37% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 15,653,427 number of insertions = 256,870 mapped reads with insertion percentage = 1.03% number of deletions = 658,309 mapped reads with deletion percentage = 2.64% homopolymer indels = 48.4% >>>>>>> Coverage mean coverageData = 0.6793X std coverageData = 6.956X There is a 27.58% of reference with a coverageData >= 1X There is a 14.19% of reference with a coverageData >= 2X There is a 7.87% of reference with a coverageData >= 3X There is a 4.78% of reference with a coverageData >= 4X There is a 3.05% of reference with a coverageData >= 5X There is a 2.03% of reference with a coverageData >= 6X There is a 1.4% of reference with a coverageData >= 7X There is a 0.99% of reference with a coverageData >= 8X There is a 0.72% of reference with a coverageData >= 9X There is a 0.53% of reference with a coverageData >= 10X There is a 0.4% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% 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 0.01% 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 176584960 0.7084634705885046 8.373348802241047 chr2 243199373 183396852 0.7541008421925496 5.995284139882695 chr3 198022430 133418287 0.6737534076316506 1.7540417237867494 chr4 191154276 97569730 0.5104239990948463 2.778417037944085 chr5 180915260 113654750 0.6282209140345596 1.559832600604003 chr6 171115067 127793095 0.7468254972544294 4.795952354078884 chr7 159138663 138788934 0.872125801383665 10.4448948944313 chr8 146364022 124579015 0.8511587294314719 2.8414868662704458 chr9 141213431 80676135 0.5713063865716852 6.219732743300001 chr10 135534747 96388004 0.7111682143030083 21.05186990416186 chr11 135006516 138724370 1.027538330075861 5.56930935004963 chr12 133851895 69150230 0.5166174898009476 1.3555966029674782 chr13 115169878 94299898 0.818789597050715 2.575360463416015 chr14 107349540 35892987 0.3343562254668255 1.549634942201887 chr15 102531392 44538467 0.4343885919348486 1.399306745424203 chr16 90354753 65137784 0.7209115385440764 12.384061529462418 chr17 81195210 45086951 0.5552907739261959 6.66758930493821 chr18 78077248 45319678 0.5804466622594076 7.929591242899402 chr19 59128983 30068770 0.5085284487304644 5.199794930785121 chr20 63025520 58727638 0.9318072742596967 2.094561207216659 chr21 48129895 18585473 0.386152369540802 1.7867805144609876 chr22 51304566 14562397 0.2838421243052714 1.0229486937916659 chrMT 16571 1302983 78.63031802546618 45.425924904521146 chrX 155270560 164036018 1.0564528008400305 3.582776084599928 chrY 59373566 4474210 0.07535693577845737 3.3580235598859036