BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818998.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 = 2,173,639 number of mapped reads = 2,143,287 (98.6%) number of supplementary alignments = 30,396 (1.4%) number of secondary alignments = 0 number of mapped bases = 198,802,491 bp number of sequenced bases = 198,687,873 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,146,342 duplication rate = 44.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2396 >>>>>>> ACTG content number of A's = 57,351,665 bp (28.87%) number of C's = 40,385,604 bp (20.33%) number of T's = 56,621,854 bp (28.5%) number of G's = 44,319,189 bp (22.31%) number of N's = 9,561 bp (0%) GC percentage = 42.63% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,285,910 number of insertions = 34,223 mapped reads with insertion percentage = 1.56% number of deletions = 62,791 mapped reads with deletion percentage = 2.87% homopolymer indels = 39.95% >>>>>>> Coverage mean coverageData = 0.0642X std coverageData = 0.7821X There is a 2.37% of reference with a coverageData >= 1X There is a 1.35% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.56% of reference with a coverageData >= 4X There is a 0.37% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% 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% 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 18741622 0.07519187685393972 1.2723657096503618 chr2 243199373 18392231 0.0756261448091809 1.0760875306900417 chr3 198022430 12533457 0.06329311785538638 0.5333993411252215 chr4 191154276 12492844 0.06535477134709768 0.5904489228031232 chr5 180915260 10092979 0.05578843376727867 0.5136389043364357 chr6 171115067 8068211 0.04715079239632358 0.6240328610914887 chr7 159138663 9309798 0.05850117013990497 0.8399589672545135 chr8 146364022 17561534 0.11998531988961057 0.8322633451577821 chr9 141213431 8010135 0.05672360584454605 0.7211585447595913 chr10 135534747 10902678 0.08044194010263656 0.9939597187002391 chr11 135006516 6620249 0.04903651465237426 0.5500777445372363 chr12 133851895 8989132 0.06715730098554078 0.5673422659736767 chr13 115169878 4034452 0.035030444331980624 0.40107560504815937 chr14 107349540 4848602 0.0451664906994478 0.46959180448948984 chr15 102531392 4909058 0.0478785853214594 0.48185516340348644 chr16 90354753 6090149 0.06740264123128088 0.8502877133325029 chr17 81195210 6799204 0.08373897918362426 0.7210518518134562 chr18 78077248 4409529 0.056476491077144524 0.8612857800407764 chr19 59128983 3722886 0.06296211791770544 1.1763561352710485 chr20 63025520 5892996 0.09350174342076036 0.6879476908380753 chr21 48129895 2647445 0.055006249234493446 0.5266532550285113 chr22 51304566 1393364 0.027158674337095064 0.3804899558446142 chrMT 16571 123410 7.447347776235592 6.949622864459921 chrX 155270560 11514574 0.07415812759353738 0.6653748882868036 chrY 59373566 701952 0.011822635008986997 0.7187416432772779