BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819020.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,598,826 number of mapped reads = 1,575,644 (98.55%) number of supplementary alignments = 23,048 (1.44%) number of secondary alignments = 0 number of mapped bases = 145,829,842 bp number of sequenced bases = 145,740,139 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 618,884 duplication rate = 31.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1643 >>>>>>> ACTG content number of A's = 40,788,683 bp (27.99%) number of C's = 30,187,629 bp (20.71%) number of T's = 42,310,747 bp (29.03%) number of G's = 32,446,419 bp (22.26%) number of N's = 6,661 bp (0%) GC percentage = 42.98% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 917,653 number of insertions = 23,359 mapped reads with insertion percentage = 1.44% number of deletions = 46,868 mapped reads with deletion percentage = 2.9% homopolymer indels = 41.01% >>>>>>> Coverage mean coverageData = 0.0471X std coverageData = 0.6151X There is a 2.48% of reference with a coverageData >= 1X There is a 1.01% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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% 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 15265831 0.061246912600470514 1.0748278251667156 chr2 243199373 11790730 0.04848174505778845 0.9197560872558751 chr3 198022430 7718048 0.03897562513499102 0.3353889813453682 chr4 191154276 7502500 0.039248402688098906 0.4062515514945938 chr5 180915260 7735426 0.04275717813964394 0.3713934768875077 chr6 171115067 6056158 0.035392312939923634 0.387782783729052 chr7 159138663 7239644 0.04549267829402337 0.7355898679844466 chr8 146364022 13178022 0.09003593793015609 0.5569781794999676 chr9 141213431 6254634 0.04429206170905939 0.5555341244190741 chr10 135534747 7339615 0.0541530136179765 0.7551837645518525 chr11 135006516 4854140 0.03595485717148645 0.37589910327510856 chr12 133851895 6590145 0.049234603663997435 0.3946406111036339 chr13 115169878 3164066 0.02747303422514696 0.2821293914918445 chr14 107349540 3410025 0.03176562284291111 0.32219813339538633 chr15 102531392 3581262 0.03492844415883869 0.32765729620755996 chr16 90354753 5171245 0.05723268370840436 0.7882770481806454 chr17 81195210 5554417 0.06840818565528681 0.5190789334965854 chr18 78077248 3461259 0.04433121157139145 0.6305692098910315 chr19 59128983 3132211 0.052972516033296224 0.8831588843177132 chr20 63025520 4301070 0.06824330842490471 0.4882067936120767 chr21 48129895 2095505 0.04353853254822185 0.3952045367302098 chr22 51304566 1277710 0.024904411042089313 0.3024942003510305 chrMT 16571 137316 8.286524651499608 7.289128544340301 chrX 155270560 8422543 0.05424430104457664 0.4528841695588693 chrY 59373566 596320 0.010043526777556194 0.7386268711053601