BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124877.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 = 3,465,796 number of mapped reads = 3,420,091 (98.68%) number of supplementary alignments = 16,212 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,710,682 number of mapped paired reads (second in pair) = 1,709,409 number of mapped paired reads (both in pair) = 3,409,556 number of mapped paired reads (singletons) = 10,535 number of mapped bases = 310,297,671 bp number of sequenced bases = 310,124,941 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 182,902 duplication rate = 3.86% >>>>>>> Insert size mean insert size = 91,159.4174 std insert size = 2,919,171.0515 median insert size = 176 >>>>>>> Mapping quality mean mapping quality = 53.3132 >>>>>>> ACTG content number of A's = 87,521,922 bp (28.22%) number of C's = 61,283,991 bp (19.76%) number of T's = 90,042,111 bp (29.03%) number of G's = 71,272,398 bp (22.98%) number of N's = 4,519 bp (0%) GC percentage = 42.74% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 2,139,705 number of insertions = 42,020 mapped reads with insertion percentage = 1.18% number of deletions = 99,102 mapped reads with deletion percentage = 2.83% homopolymer indels = 46.11% >>>>>>> Coverage mean coverageData = 0.1002X std coverageData = 0.7891X There is a 6.77% of reference with a coverageData >= 1X There is a 1.96% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 21797374 0.08745163367115542 0.6917612414278542 chr2 243199373 28779808 0.11833833140680013 1.1430291496859286 chr3 198022430 22167149 0.11194261680356109 0.4520856972745996 chr4 191154276 14354150 0.07509196393807063 0.6490961268182642 chr5 180915260 13925105 0.07697031748455051 0.40083812606068564 chr6 171115067 13997961 0.08180437436289582 0.44055507596156457 chr7 159138663 19661185 0.12354750649124153 1.1721106112829414 chr8 146364022 15446172 0.1055325741185221 0.47756471609468687 chr9 141213431 16954050 0.12005975550583428 0.8050379295860799 chr10 135534747 12920929 0.09533296284531376 1.502050837131231 chr11 135006516 16251747 0.12037750089040147 0.6042074026266525 chr12 133851895 15771023 0.11782442826080274 0.48251754515098033 chr13 115169878 6444175 0.05595364961661243 0.31769659296731717 chr14 107349540 10262434 0.09559830438025166 0.4522469020032912 chr15 102531392 10023328 0.09775862596306115 0.4260222981642313 chr16 90354753 11331350 0.12540956201828143 1.3427540731959402 chr17 81195210 13187968 0.16242298037039377 1.2965474021412784 chr18 78077248 8388349 0.1074365351606655 0.8827269205466599 chr19 59128983 5427511 0.09179104264316537 0.543924924504609 chr20 63025520 6109973 0.09694442822526494 0.4934525501789009 chr21 48129895 4025317 0.08363444383163521 0.4572849491372898 chr22 51304566 3194810 0.0622714555269798 0.379067709544517 chrMT 16571 299733 18.087803994930905 10.156934434577023 chrX 155270560 18739702 0.1206906318879767 0.579075048851086 chrY 59373566 836368 0.014086538106874026 0.9510571707193002