BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927013.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 18,699,628 number of mapped reads = 18,228,353 (97.48%) number of supplementary alignments = 575,048 (3.08%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,127,685 number of mapped paired reads (second in pair) = 9,100,668 number of mapped paired reads (both in pair) = 17,968,016 number of mapped paired reads (singletons) = 260,337 number of mapped bases = 1,662,697,583 bp number of sequenced bases = 1,661,411,754 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,234,553 duplication rate = 5.25% >>>>>>> Insert size mean insert size = 316,723.3915 std insert size = 5,472,548.1861 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 52.5187 >>>>>>> ACTG content number of A's = 473,911,307 bp (28.52%) number of C's = 324,109,769 bp (19.51%) number of T's = 483,171,098 bp (29.08%) number of G's = 379,908,462 bp (22.87%) number of N's = 311,118 bp (0.02%) GC percentage = 42.37% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 15,879,683 number of insertions = 289,765 mapped reads with insertion percentage = 1.56% number of deletions = 873,899 mapped reads with deletion percentage = 4.67% homopolymer indels = 51.8% >>>>>>> Coverage mean coverageData = 0.5371X std coverageData = 2.3336X There is a 27.93% of reference with a coverageData >= 1X There is a 12.59% of reference with a coverageData >= 2X There is a 5.78% of reference with a coverageData >= 3X There is a 2.91% of reference with a coverageData >= 4X There is a 1.52% of reference with a coverageData >= 5X There is a 0.83% of reference with a coverageData >= 6X There is a 0.47% of reference with a coverageData >= 7X There is a 0.28% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% 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 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% 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 111529745 0.4474602492565104 2.8505471804369997 chr2 243199373 149418856 0.6143883273909592 3.777278981424731 chr3 198022430 116223719 0.5869219916147883 1.2183930721197018 chr4 191154276 102395758 0.5356707688819893 1.9667754390604297 chr5 180915260 101214904 0.5594602909671633 1.1583285713843132 chr6 171115067 96407259 0.5634060208152214 1.4106330859071146 chr7 159138663 86920606 0.5461941451650879 1.6687527249283605 chr8 146364022 86554920 0.59136746050884 1.4341860890060127 chr9 141213431 71173910 0.5040165761569804 2.685500694101837 chr10 135534747 82668794 0.6099453891333121 5.303898261021635 chr11 135006516 82235721 0.6091240884995507 2.4800208094974057 chr12 133851895 78517088 0.5865967605464233 1.2384951902930685 chr13 115169878 50482302 0.4383290394733248 1.0214967171803249 chr14 107349540 51593045 0.48060797465923005 1.1243577151995277 chr15 102531392 49176421 0.4796230699764615 1.1076972835591732 chr16 90354753 50867518 0.5629755636651456 3.2288914246313163 chr17 81195210 41141565 0.5066994099775097 1.401680217232419 chr18 78077248 43452445 0.556531462276949 2.744182725766567 chr19 59128983 27742611 0.469188029159913 1.938487491099329 chr20 63025520 39842149 0.6321589889301984 1.3707428765326926 chr21 48129895 20801475 0.4321944812054961 1.5548613005935004 chr22 51304566 20639665 0.4022968443003689 1.0770225524206778 chrMT 16571 98483 5.9430933558626515 5.910550593403312 chrX 155270560 98536209 0.6346097354192578 1.462482663962964 chrY 59373566 3062415 0.051578761498004014 1.782701277376737