BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472801.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 114,678,784 number of mapped reads = 114,175,897 (99.56%) number of supplementary alignments = 94,248 (0.08%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 57,257,320 number of mapped paired reads (second in pair) = 56,918,577 number of mapped paired reads (both in pair) = 113,795,946 number of mapped paired reads (singletons) = 379,951 number of mapped bases = 11,330,369,639 bp number of sequenced bases = 11,328,958,762 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,033,121 duplication rate = 48.16% >>>>>>> Insert size mean insert size = 14,786.0357 std insert size = 1,205,681.5241 median insert size = 246 >>>>>>> Mapping quality mean mapping quality = 53.6935 >>>>>>> ACTG content number of A's = 3,191,394,172 bp (28.17%) number of C's = 2,466,425,700 bp (21.77%) number of T's = 3,243,316,863 bp (28.63%) number of G's = 2,426,656,583 bp (21.42%) number of N's = 1,165,444 bp (0.01%) GC percentage = 43.19% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 46,957,779 number of insertions = 506,806 mapped reads with insertion percentage = 0.44% number of deletions = 600,576 mapped reads with deletion percentage = 0.52% homopolymer indels = 46.15% >>>>>>> Coverage mean coverageData = 3.66X std coverageData = 25.2172X There is a 16.48% of reference with a coverageData >= 1X There is a 9.05% of reference with a coverageData >= 2X There is a 6.11% of reference with a coverageData >= 3X There is a 5.31% of reference with a coverageData >= 4X There is a 4.81% of reference with a coverageData >= 5X There is a 4.57% of reference with a coverageData >= 6X There is a 4.38% of reference with a coverageData >= 7X There is a 4.23% of reference with a coverageData >= 8X There is a 4.11% of reference with a coverageData >= 9X There is a 4% of reference with a coverageData >= 10X There is a 3.9% of reference with a coverageData >= 11X There is a 3.8% of reference with a coverageData >= 12X There is a 3.72% of reference with a coverageData >= 13X There is a 3.64% of reference with a coverageData >= 14X There is a 3.56% of reference with a coverageData >= 15X There is a 3.49% of reference with a coverageData >= 16X There is a 3.42% of reference with a coverageData >= 17X There is a 3.36% of reference with a coverageData >= 18X There is a 3.3% of reference with a coverageData >= 19X There is a 3.24% of reference with a coverageData >= 20X There is a 3.18% of reference with a coverageData >= 21X There is a 3.13% of reference with a coverageData >= 22X There is a 3.07% of reference with a coverageData >= 23X There is a 3.02% of reference with a coverageData >= 24X There is a 2.97% of reference with a coverageData >= 25X There is a 2.93% of reference with a coverageData >= 26X There is a 2.88% of reference with a coverageData >= 27X There is a 2.83% of reference with a coverageData >= 28X There is a 2.79% of reference with a coverageData >= 29X There is a 2.75% of reference with a coverageData >= 30X There is a 2.71% of reference with a coverageData >= 31X There is a 2.67% of reference with a coverageData >= 32X There is a 2.63% of reference with a coverageData >= 33X There is a 2.59% of reference with a coverageData >= 34X There is a 2.55% of reference with a coverageData >= 35X There is a 2.52% of reference with a coverageData >= 36X There is a 2.48% of reference with a coverageData >= 37X There is a 2.45% of reference with a coverageData >= 38X There is a 2.41% of reference with a coverageData >= 39X There is a 2.38% of reference with a coverageData >= 40X There is a 2.35% of reference with a coverageData >= 41X There is a 2.32% of reference with a coverageData >= 42X There is a 2.29% of reference with a coverageData >= 43X There is a 2.26% of reference with a coverageData >= 44X There is a 2.23% of reference with a coverageData >= 45X There is a 2.2% of reference with a coverageData >= 46X There is a 2.17% of reference with a coverageData >= 47X There is a 2.14% of reference with a coverageData >= 48X There is a 2.11% of reference with a coverageData >= 49X There is a 2.09% of reference with a coverageData >= 50X There is a 2.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1162649034 4.664578284039662 29.9454041352853 chr2 243199373 1030155763 4.235848761830484 30.397173261069874 chr3 198022430 705838102 3.5644351096994416 24.097194360702076 chr4 191154276 540913339 2.8297213660028198 21.998139721681927 chr5 180915260 564406763 3.11972999403146 22.67892545429804 chr6 171115067 586475127 3.4273728040558815 23.883006393144427 chr7 159138663 621872725 3.907741294772597 27.481018651432557 chr8 146364022 419990775 2.8694946289464496 21.84870041269706 chr9 141213431 495251936 3.5071163733710287 25.386010346324646 chr10 135534747 520652296 3.841467280711418 26.803187651606958 chr11 135006516 538416580 3.9880784717087283 24.075007760869457 chr12 133851895 604512009 4.516275313098855 26.584159553885065 chr13 115169878 270685145 2.350311988695516 20.585052976601066 chr14 107349540 359509809 3.3489645973331603 23.9462802033928 chr15 102531392 408566136 3.984790687324327 25.347667865139154 chr16 90354753 407970523 4.515208214890477 28.541311893631757 chr17 81195210 515296977 6.346396259089668 30.038125261306845 chr18 78077248 201871869 2.5855402716038354 20.565191987695705 chr19 59128983 430149849 7.274771646250029 31.342357602830518 chr20 63025520 258933452 4.10839056940744 25.488342624809928 chr21 48129895 129673293 2.694235942131185 23.779176729436383 chr22 51304566 176186281 3.4341247716626238 22.21227874062352 chrMT 16571 2231736 134.67720716915093 381.61179445248905 chrX 155270560 316215340 2.0365440815052125 16.408226153319703 chrY 59373566 61944780 1.043305702743204 16.103982343866477