BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013298.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,096,355 number of mapped reads = 1,851,594 (88.32%) number of supplementary alignments = 11,374 (0.54%) number of secondary alignments = 0 number of mapped bases = 122,686,962 bp number of sequenced bases = 122,633,683 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,725 duplication rate = 3.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5706 >>>>>>> ACTG content number of A's = 34,283,671 bp (27.96%) number of C's = 22,416,177 bp (18.28%) number of T's = 38,971,003 bp (31.78%) number of G's = 26,936,192 bp (21.96%) number of N's = 26,640 bp (0.02%) GC percentage = 40.24% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 997,623 number of insertions = 8,960 mapped reads with insertion percentage = 0.48% number of deletions = 31,077 mapped reads with deletion percentage = 1.66% homopolymer indels = 46.62% >>>>>>> Coverage mean coverageData = 0.0396X std coverageData = 0.3653X There is a 3.37% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 10117678 0.0405923883335079 0.7329964871114353 chr2 243199373 18441816 0.07583003102561453 0.4599600361050028 chr3 198022430 8500460 0.04292675329759361 0.23600060790732996 chr4 191154276 6098854 0.031905401896424226 0.20976759972290557 chr5 180915260 5326293 0.02944081665637271 0.19490711441846756 chr6 171115067 5863942 0.0342689986498968 0.25179008883869564 chr7 159138663 7505376 0.04716249249875877 0.5221295348921776 chr8 146364022 6481647 0.044284428040656056 0.3752099598482505 chr9 141213431 3781223 0.026776652710888384 0.27102593269691355 chr10 135534747 6355270 0.04689033728007771 0.3843922876152003 chr11 135006516 5190346 0.038445151788081104 0.2768732254312077 chr12 133851895 5001223 0.037363856522165784 0.22368889509588374 chr13 115169878 4655991 0.040427159261208906 0.22808477669842603 chr14 107349540 5683566 0.05294448397263742 0.2769035817513507 chr15 102531392 1727815 0.016851570687736298 0.1514923862238584 chr16 90354753 5684873 0.06291725461304731 0.30818677919978354 chr17 81195210 2052225 0.025275197884210166 0.18802835928998698 chr18 78077248 3060704 0.039200971837531975 0.47006638408510343 chr19 59128983 1727383 0.02921381211647087 0.574417796795412 chr20 63025520 2222124 0.03525752742698513 0.21738503486593452 chr21 48129895 1876444 0.03898707861299095 0.23572783846433257 chr22 51304566 1208363 0.023552737976576976 0.17104473262847525 chrMT 16571 17428 1.0517168547462434 1.360157397929301 chrX 155270560 3901306 0.02512585772859968 0.19572221440680304 chrY 59373566 204612 0.003446180072795358 0.09571519581451957