BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124953.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 = 6,649,326 number of mapped reads = 6,237,107 (93.8%) number of supplementary alignments = 7,753 (0.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,186,635 number of mapped paired reads (second in pair) = 3,050,472 number of mapped paired reads (both in pair) = 6,048,250 number of mapped paired reads (singletons) = 188,857 number of mapped bases = 387,356,177 bp number of sequenced bases = 387,206,054 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 536,315 duplication rate = 5.17% >>>>>>> Insert size mean insert size = 25,271.856 std insert size = 1,457,666.8097 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 51.6768 >>>>>>> ACTG content number of A's = 107,822,297 bp (27.85%) number of C's = 68,024,822 bp (17.57%) number of T's = 117,892,423 bp (30.45%) number of G's = 93,463,320 bp (24.14%) number of N's = 3,192 bp (0%) GC percentage = 41.71% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 2,406,707 number of insertions = 39,687 mapped reads with insertion percentage = 0.63% number of deletions = 101,019 mapped reads with deletion percentage = 1.6% homopolymer indels = 48.99% >>>>>>> Coverage mean coverageData = 0.1251X std coverageData = 1.6864X There is a 9.25% of reference with a coverageData >= 1X There is a 1.87% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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% 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 31027897 0.12448473297885986 1.8989611909128425 chr2 243199373 33625057 0.13826128161934037 1.6335591318429254 chr3 198022430 23484695 0.11859613580138371 0.4789435739966329 chr4 191154276 18538972 0.09698434368269115 2.961120161131959 chr5 180915260 20535690 0.11350999357378698 0.5933517712868305 chr6 171115067 27308106 0.15958913775839506 1.2126085540640987 chr7 159138663 26543037 0.16679188136700634 2.286994363799869 chr8 146364022 22527377 0.1539133503724023 0.7045399643325589 chr9 141213431 15250042 0.10799285798813286 1.8707131999764033 chr10 135534747 18213950 0.13438583391460493 3.909651026126001 chr11 135006516 25116434 0.18603867979231462 1.349891424768902 chr12 133851895 12269890 0.09166765999091757 0.3876090801500707 chr13 115169878 15376255 0.13350934521264318 0.5852504820675699 chr14 107349540 6269915 0.0584065381183748 0.540137744825398 chr15 102531392 7615718 0.0742769394957595 0.34579184672607266 chr16 90354753 12124820 0.13419128045206433 2.6519235014098106 chr17 81195210 7485683 0.0921936528029178 1.153311154091399 chr18 78077248 10967515 0.14047005089113795 2.026135329159789 chr19 59128983 5533982 0.09359169935325963 1.4267016604323741 chr20 63025520 8987869 0.14260682022139604 0.5015309514351638 chr21 48129895 3381314 0.07025392430214111 0.4551579705792219 chr22 51304566 2350955 0.045823504286148724 0.2640207282950159 chrMT 16571 227099 13.704604429424899 9.236779860780057 chrX 155270560 31658662 0.20389352624219298 0.9639707012831994 chrY 59373566 935243 0.015751841484474758 0.7413572336269892