BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038491.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 11,300,066 number of mapped reads = 10,620,151 (93.98%) number of supplementary alignments = 196,662 (1.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,386,033 number of mapped paired reads (second in pair) = 5,234,118 number of mapped paired reads (both in pair) = 10,449,312 number of mapped paired reads (singletons) = 170,839 number of mapped bases = 1,508,841,801 bp number of sequenced bases = 1,507,648,320 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,507,543 duplication rate = 8.78% >>>>>>> Insert size mean insert size = 84,540.9222 std insert size = 2,712,849.7031 median insert size = 261 >>>>>>> Mapping quality mean mapping quality = 53.6931 >>>>>>> ACTG content number of A's = 437,140,764 bp (28.99%) number of C's = 308,698,759 bp (20.48%) number of T's = 438,753,646 bp (29.1%) number of G's = 323,021,414 bp (21.43%) number of N's = 33,737 bp (0%) GC percentage = 41.9% >>>>>>> Mismatches and indels general error rate = 0.0149 number of mismatches = 21,600,410 number of insertions = 292,545 mapped reads with insertion percentage = 2.55% number of deletions = 558,534 mapped reads with deletion percentage = 5.02% homopolymer indels = 45.73% >>>>>>> Coverage mean coverageData = 0.4874X std coverageData = 6.8698X There is a 21.8% of reference with a coverageData >= 1X There is a 10.9% of reference with a coverageData >= 2X There is a 5.39% of reference with a coverageData >= 3X There is a 2.99% of reference with a coverageData >= 4X There is a 1.66% of reference with a coverageData >= 5X There is a 0.97% of reference with a coverageData >= 6X There is a 0.58% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% 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 0.02% 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 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 98900112 0.39678983186966665 5.028590571804857 chr2 243199373 97285300 0.4000228240720012 7.511271372935955 chr3 198022430 105818160 0.5343746160472831 1.2892566954287221 chr4 191154276 94395336 0.4938175487112828 6.385756802166438 chr5 180915260 92968985 0.5138813884467236 1.3855883149413317 chr6 171115067 86275840 0.504197798081685 6.915407137808338 chr7 159138663 114809279 0.7214417718213455 7.1498901014151715 chr8 146364022 70365228 0.48075494946428843 1.7805118010985181 chr9 141213431 64405184 0.45608398254979016 8.877327383811714 chr10 135534747 71064740 0.5243285694110603 19.90454599703762 chr11 135006516 90166855 0.6678703937519579 4.116883648836037 chr12 133851895 55646539 0.4157321717410127 1.137741159906966 chr13 115169878 106798000 0.9273084408407553 1.855112185137477 chr14 107349540 29615017 0.27587465209445705 1.0501845212485865 chr15 102531392 28266835 0.2756895663720239 0.8474370632853327 chr16 90354753 60938480 0.6744357986347437 13.767052452186492 chr17 81195210 36296805 0.44703135813060896 3.4670108830876356 chr18 78077248 24540714 0.31431325550818595 7.619399714807317 chr19 59128983 19786077 0.33462569447541485 2.9946192284208597 chr20 63025520 52046618 0.825802278188264 2.557518191926754 chr21 48129895 14114664 0.2932618905567943 3.0952647221157923 chr22 51304566 9993937 0.19479624873934223 0.95722230336008 chrMT 16571 1393152 84.07169150926318 35.49808472857105 chrX 155270560 59232015 0.38147614718463047 1.4324169894456353 chrY 59373566 23717929 0.39946950466138414 11.84607636279453