BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006380.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 = 6,962,470 number of mapped reads = 6,186,962 (88.86%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,135,891 number of mapped paired reads (second in pair) = 3,051,071 number of mapped paired reads (both in pair) = 5,689,088 number of mapped paired reads (singletons) = 497,874 number of mapped bases = 239,645,345 bp number of sequenced bases = 239,615,776 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 209,016 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 67,557.139 std insert size = 2,471,912.0724 median insert size = 148 >>>>>>> Mapping quality mean mapping quality = 48.4238 >>>>>>> ACTG content number of A's = 67,494,591 bp (28.17%) number of C's = 51,040,774 bp (21.3%) number of T's = 68,291,378 bp (28.5%) number of G's = 52,778,832 bp (22.03%) number of N's = 10,201 bp (0%) GC percentage = 43.33% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 881,294 number of insertions = 6,380 mapped reads with insertion percentage = 0.1% number of deletions = 22,225 mapped reads with deletion percentage = 0.36% homopolymer indels = 44.85% >>>>>>> Coverage mean coverageData = 0.0774X std coverageData = 0.4199X There is a 6.57% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 19311838 0.07747959833568478 0.5530983175052061 chr2 243199373 21284835 0.08752010639435324 0.41038238396932997 chr3 198022430 16028219 0.08094143173578872 0.32012124116115664 chr4 191154276 14982600 0.07837962254111439 0.35975475605064666 chr5 180915260 14794079 0.08177352756201992 0.3222672071812495 chr6 171115067 13627766 0.07964094710607804 0.3472055442908694 chr7 159138663 12460087 0.07829704463459015 0.47209354160146416 chr8 146364022 12427234 0.08490634399210484 0.8276117061679629 chr9 141213431 9970447 0.07060551485361191 0.34817846506236805 chr10 135534747 11191853 0.08257552581700692 0.47333104142205273 chr11 135006516 11056940 0.08189930625274412 0.3814679844218548 chr12 133851895 10661031 0.0796479646403213 0.3211895092364134 chr13 115169878 7433826 0.06454661695482564 0.2861055838227385 chr14 107349540 7180270 0.06688682597056309 0.3164722369828884 chr15 102531392 6865776 0.0669626722711421 0.2947057802918365 chr16 90354753 7161817 0.07926331224656218 0.385941230509873 chr17 81195210 6569474 0.08090962508748976 0.3370916047154127 chr18 78077248 6309327 0.08080877799381454 0.5409121976440865 chr19 59128983 4911530 0.08306467912698583 0.45822050363858047 chr20 63025520 5221653 0.08284982019981747 0.3351161744907519 chr21 48129895 3136620 0.06516989077162956 0.3384461142603694 chr22 51304566 3071774 0.05987330640317667 0.2827386925588604 chrMT 16571 11518 0.6950697000784503 0.9725018732415043 chrX 155270560 13381981 0.08618492133988569 0.35683089420471503 chrY 59373566 592850 0.009985083260789828 0.2446947590003958