BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777262.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 3,249,222 number of mapped reads = 3,151,416 (96.99%) number of supplementary alignments = 53,914 (1.66%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,580,916 number of mapped paired reads (second in pair) = 1,570,500 number of mapped paired reads (both in pair) = 3,132,942 number of mapped paired reads (singletons) = 18,474 number of mapped bases = 235,995,325 bp number of sequenced bases = 235,953,541 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,290 duplication rate = 1.36% >>>>>>> Insert size mean insert size = 168,728.4996 std insert size = 3,900,762.0734 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 52.7302 >>>>>>> ACTG content number of A's = 70,134,590 bp (29.72%) number of C's = 48,104,203 bp (20.39%) number of T's = 68,659,571 bp (29.1%) number of G's = 49,041,547 bp (20.78%) number of N's = 13,630 bp (0.01%) GC percentage = 41.17% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 1,312,345 number of insertions = 45,138 mapped reads with insertion percentage = 1.42% number of deletions = 21,460 mapped reads with deletion percentage = 0.67% homopolymer indels = 49.61% >>>>>>> Coverage mean coverageData = 0.0762X std coverageData = 0.3539X There is a 6.43% of reference with a coverageData >= 1X There is a 1.02% of reference with a coverageData >= 2X There is a 0.1% 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 17416714 0.06987631136132656 0.4102979846648508 chr2 243199373 22875044 0.09405881157432096 0.3565371426291181 chr3 198022430 16475596 0.08320065560249917 0.32283249662749575 chr4 191154276 15179639 0.07941040774834668 0.31612320647622183 chr5 180915260 13640200 0.07539551942716165 0.3073152236772944 chr6 171115067 11613803 0.06787130557007 0.3197985812200757 chr7 159138663 16336732 0.10265721536192622 0.3791974054720627 chr8 146364022 12178407 0.08320628822293501 0.3300531759526702 chr9 141213431 8850065 0.06267155282134601 0.3361404732185496 chr10 135534747 10869844 0.08019968488228336 0.37707243263653933 chr11 135006516 14199597 0.10517712345084144 0.3719609729240147 chr12 133851895 11160054 0.08337613748389591 0.32263259056247245 chr13 115169878 10430271 0.09056422721920397 0.3385176417327481 chr14 107349540 4937645 0.04599595862264524 0.2396583076467825 chr15 102531392 9052578 0.08829079390631896 0.3349208767263723 chr16 90354753 6240729 0.06906918333338811 0.30963601179162875 chr17 81195210 5723805 0.07049436783278225 0.3196798852570699 chr18 78077248 5270225 0.06750013781223436 0.3724590662289224 chr19 59128983 4243328 0.07176392666858485 0.34698910838096003 chr20 63025520 6346319 0.10069443298524153 0.35677315685204464 chr21 48129895 2158267 0.04484254536603498 0.24577280062299478 chr22 51304566 1778737 0.034670150021345075 0.20866385874094687 chrMT 16571 819351 49.444873574316574 12.098182554038253 chrX 155270560 7915624 0.05097955465607904 0.2551512386095775 chrY 59373566 282751 0.004762237120808947 0.12361850773102312