BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975226.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 38,337,872 number of mapped reads = 38,280,939 (99.85%) number of supplementary alignments = 114,893 (0.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 19,142,522 number of mapped paired reads (second in pair) = 19,138,417 number of mapped paired reads (both in pair) = 38,245,472 number of mapped paired reads (singletons) = 35,467 number of mapped bases = 3,744,465,969 bp number of sequenced bases = 3,743,987,277 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,338,587 duplication rate = 35.87% >>>>>>> Insert size mean insert size = 203,691.3351 std insert size = 4,465,648.7624 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 56.2464 >>>>>>> ACTG content number of A's = 976,397,877 bp (26.08%) number of C's = 879,294,090 bp (23.49%) number of T's = 1,007,505,676 bp (26.91%) number of G's = 880,693,254 bp (23.52%) number of N's = 96,380 bp (0%) GC percentage = 47.01% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 14,508,404 number of insertions = 231,026 mapped reads with insertion percentage = 0.6% number of deletions = 216,626 mapped reads with deletion percentage = 0.56% homopolymer indels = 37.34% >>>>>>> Coverage mean coverageData = 1.2096X std coverageData = 9.2909X There is a 10.71% of reference with a coverageData >= 1X There is a 5.6% of reference with a coverageData >= 2X There is a 4.04% of reference with a coverageData >= 3X There is a 3.51% of reference with a coverageData >= 4X There is a 3.21% of reference with a coverageData >= 5X There is a 3.01% of reference with a coverageData >= 6X There is a 2.85% of reference with a coverageData >= 7X There is a 2.72% of reference with a coverageData >= 8X There is a 2.59% of reference with a coverageData >= 9X There is a 2.48% of reference with a coverageData >= 10X There is a 2.38% of reference with a coverageData >= 11X There is a 2.29% of reference with a coverageData >= 12X There is a 2.2% of reference with a coverageData >= 13X There is a 2.12% of reference with a coverageData >= 14X There is a 2.04% of reference with a coverageData >= 15X There is a 1.97% of reference with a coverageData >= 16X There is a 1.9% of reference with a coverageData >= 17X There is a 1.83% of reference with a coverageData >= 18X There is a 1.77% of reference with a coverageData >= 19X There is a 1.71% of reference with a coverageData >= 20X There is a 1.65% of reference with a coverageData >= 21X There is a 1.59% of reference with a coverageData >= 22X There is a 1.54% of reference with a coverageData >= 23X There is a 1.49% of reference with a coverageData >= 24X There is a 1.44% of reference with a coverageData >= 25X There is a 1.4% of reference with a coverageData >= 26X There is a 1.35% of reference with a coverageData >= 27X There is a 1.31% of reference with a coverageData >= 28X There is a 1.27% of reference with a coverageData >= 29X There is a 1.23% of reference with a coverageData >= 30X There is a 1.19% of reference with a coverageData >= 31X There is a 1.15% of reference with a coverageData >= 32X There is a 1.12% of reference with a coverageData >= 33X There is a 1.08% of reference with a coverageData >= 34X There is a 1.05% of reference with a coverageData >= 35X There is a 1.02% of reference with a coverageData >= 36X There is a 0.99% of reference with a coverageData >= 37X There is a 0.96% of reference with a coverageData >= 38X There is a 0.93% of reference with a coverageData >= 39X There is a 0.9% of reference with a coverageData >= 40X There is a 0.87% of reference with a coverageData >= 41X There is a 0.85% of reference with a coverageData >= 42X There is a 0.82% of reference with a coverageData >= 43X There is a 0.8% of reference with a coverageData >= 44X There is a 0.78% of reference with a coverageData >= 45X There is a 0.75% of reference with a coverageData >= 46X There is a 0.73% of reference with a coverageData >= 47X There is a 0.71% of reference with a coverageData >= 48X There is a 0.69% of reference with a coverageData >= 49X There is a 0.67% of reference with a coverageData >= 50X There is a 0.65% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 382870092 1.5360848067856971 10.854387171432819 chr2 243199373 300525641 1.2357171702083294 9.367256456445778 chr3 198022430 240139022 1.2126859669381898 9.176356678433914 chr4 191154276 178795252 0.9353452914649945 8.428215901589224 chr5 180915260 190851398 1.054921503028545 8.555867215753548 chr6 171115067 221071034 1.2919437070962314 10.215278055062312 chr7 159138663 187524886 1.1783741453200471 9.59811794604478 chr8 146364022 138925502 0.9491779475696561 7.842229078621741 chr9 141213431 148289085 1.0501060979107575 8.444414680829212 chr10 135534747 156197229 1.152451548088993 8.948722070789746 chr11 135006516 223963355 1.6589077448676626 11.499345874941957 chr12 133851895 207965795 1.5537007899664028 10.628229187475423 chr13 115169878 81794285 0.7102055365553135 7.257627125902948 chr14 107349540 124690920 1.1615412604469475 9.20189005632922 chr15 102531392 127759255 1.2460501365279426 9.331479800299132 chr16 90354753 128030340 1.4169740467333245 9.484399940672796 chr17 81195210 183668383 2.262059338229435 12.421987287692554 chr18 78077248 65873238 0.8436931332415815 7.607989278619076 chr19 59128983 174299942 2.947791982148585 13.827427554670942 chr20 63025520 85075931 1.3498648007981529 9.542845708579753 chr21 48129895 40445034 0.8403308172602496 8.00268222893654 chr22 51304566 64000719 1.2474663366219685 8.400370640154438 chrMT 16571 400928 24.194556755778166 39.957322552643085 chrX 155270560 85614495 0.5513891042835165 4.9897977665393425 chrY 59373566 5694208 0.09590476677786205 1.5071001078248458