BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124864.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 = 5,052,750 number of mapped reads = 4,982,342 (98.61%) number of supplementary alignments = 23,353 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,497,689 number of mapped paired reads (second in pair) = 2,484,653 number of mapped paired reads (both in pair) = 4,954,170 number of mapped paired reads (singletons) = 28,172 number of mapped bases = 430,042,097 bp number of sequenced bases = 429,805,365 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 470,507 duplication rate = 5.7% >>>>>>> Insert size mean insert size = 28,491.5742 std insert size = 1,516,979.6621 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 52.5609 >>>>>>> ACTG content number of A's = 122,752,007 bp (28.56%) number of C's = 78,350,569 bp (18.23%) number of T's = 130,013,287 bp (30.25%) number of G's = 98,524,096 bp (22.92%) number of N's = 165,406 bp (0.04%) GC percentage = 41.15% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 3,563,376 number of insertions = 62,051 mapped reads with insertion percentage = 1.21% number of deletions = 137,773 mapped reads with deletion percentage = 2.71% homopolymer indels = 47.58% >>>>>>> Coverage mean coverageData = 0.1389X std coverageData = 1.842X There is a 9.53% of reference with a coverageData >= 1X There is a 2.51% of reference with a coverageData >= 2X There is a 0.67% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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% 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 34785004 0.13955834437018313 1.7729683792528848 chr2 243199373 32070631 0.1318697108647562 1.7891434497816134 chr3 198022430 32232615 0.1627725455141622 0.5382796096459449 chr4 191154276 26224134 0.13718832007712975 1.3846797115101368 chr5 180915260 33520769 0.18528436462463144 0.5685663073136635 chr6 171115067 25505968 0.14905740591505012 2.3585594023828937 chr7 159138663 20456358 0.1285442369212314 1.8961071822573605 chr8 146364022 30085564 0.20555300126966994 0.8612622639559719 chr9 141213431 21539734 0.15253318220134457 2.3366235181538917 chr10 135534747 22660003 0.16718962112350422 5.235549708437896 chr11 135006516 16012223 0.11860333467163911 1.3550962159775344 chr12 133851895 15903326 0.11881285655313285 0.4528668826901267 chr13 115169878 8868472 0.07700339840596167 0.3412251636569057 chr14 107349540 17364280 0.1617545822739436 0.687971025064279 chr15 102531392 10441381 0.10183594308365579 0.41530684099067017 chr16 90354753 12732078 0.1409121001083363 3.0242740522311675 chr17 81195210 12414881 0.15290164284321697 1.3329928719229411 chr18 78077248 10287341 0.13175849896758657 2.5005681815809333 chr19 59128983 4386491 0.07418512508493508 1.2398887615463734 chr20 63025520 10050366 0.15946502305732663 0.6284724059327073 chr21 48129895 5599206 0.11633530469991675 1.0100244723507028 chr22 51304566 2563647 0.049969178181918546 0.29275158135914275 chrMT 16571 121575 7.336612153762597 5.04002813691221 chrX 155270560 22415120 0.1443616871092627 0.7693420782886184 chrY 59373566 1800930 0.030332185201744494 2.084863557385764