BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006060.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 4,194,814 number of mapped reads = 3,697,920 (88.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,882,549 number of mapped paired reads (second in pair) = 1,815,371 number of mapped paired reads (both in pair) = 3,411,440 number of mapped paired reads (singletons) = 286,480 number of mapped bases = 142,899,378 bp number of sequenced bases = 142,884,360 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 160,512 duplication rate = 3.93% >>>>>>> Insert size mean insert size = 73,270.0972 std insert size = 2,676,130.2566 median insert size = 96 >>>>>>> Mapping quality mean mapping quality = 46.1175 >>>>>>> ACTG content number of A's = 36,797,706 bp (25.75%) number of C's = 33,195,424 bp (23.23%) number of T's = 38,089,521 bp (26.66%) number of G's = 34,794,815 bp (24.35%) number of N's = 6,894 bp (0%) GC percentage = 47.58% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 606,144 number of insertions = 4,538 mapped reads with insertion percentage = 0.12% number of deletions = 11,578 mapped reads with deletion percentage = 0.31% homopolymer indels = 43.01% >>>>>>> Coverage mean coverageData = 0.0462X std coverageData = 0.3132X There is a 3.25% of reference with a coverageData >= 1X There is a 0.91% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 12348176 0.049541204553307815 0.3204184569551639 chr2 243199373 12160534 0.050002324635927416 0.3557250800210975 chr3 198022430 9685502 0.048911135975858895 0.2957644454036769 chr4 191154276 8423525 0.04406663129000578 0.29274391542230804 chr5 180915260 8306756 0.04591517597796891 0.2883823359115454 chr6 171115067 8018600 0.046860864683529006 0.30634342761527816 chr7 159138663 7635801 0.04798206077677051 0.3336434071464094 chr8 146364022 7108044 0.04856414782042543 0.3287043310315121 chr9 141213431 6163898 0.043649516595910764 0.29039110628854975 chr10 135534747 7081557 0.05224901478585414 0.3251864554484545 chr11 135006516 6642867 0.04920404730687221 0.3807570460554369 chr12 133851895 6643733 0.0496349566063297 0.3034376112656378 chr13 115169878 4237366 0.03679231126736107 0.26283490645005675 chr14 107349540 4514045 0.04204997059139704 0.282004078271615 chr15 102531392 4493467 0.04382528035901434 0.28530678755328487 chr16 90354753 4839154 0.05355727108235247 0.36280919268967965 chr17 81195210 4535778 0.05586263032018761 0.33936752054303604 chr18 78077248 3656133 0.04682712433716926 0.31886132646850623 chr19 59128983 3623557 0.06128224799672269 0.408048615400849 chr20 63025520 3532103 0.05604242535404706 0.3321471310535806 chr21 48129895 1885828 0.03918205098930717 0.29305547063589116 chr22 51304566 2222488 0.04331949713793505 0.32216445677956057 chrMT 16571 40561 2.447709854565204 3.6256101303103256 chrX 155270560 4160394 0.026794480550595037 0.21930314945801893 chrY 59373566 939511 0.015823725325846187 0.20620810201488848