BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472640.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 16,314,796 number of mapped reads = 16,208,948 (99.35%) number of supplementary alignments = 77,924 (0.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,125,218 number of mapped paired reads (second in pair) = 8,083,730 number of mapped paired reads (both in pair) = 16,136,204 number of mapped paired reads (singletons) = 72,744 number of mapped bases = 1,595,592,834 bp number of sequenced bases = 1,595,340,991 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,491,197 duplication rate = 48.67% >>>>>>> Insert size mean insert size = 19,039.9477 std insert size = 1,323,500.5217 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 54.7601 >>>>>>> ACTG content number of A's = 424,927,371 bp (26.64%) number of C's = 374,784,977 bp (23.49%) number of T's = 425,494,499 bp (26.67%) number of G's = 369,831,032 bp (23.18%) number of N's = 303,112 bp (0.02%) GC percentage = 46.67% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 9,522,242 number of insertions = 99,448 mapped reads with insertion percentage = 0.61% number of deletions = 88,790 mapped reads with deletion percentage = 0.54% homopolymer indels = 46.09% >>>>>>> Coverage mean coverageData = 0.5154X std coverageData = 28.6266X There is a 3.27% of reference with a coverageData >= 1X There is a 1.52% of reference with a coverageData >= 2X There is a 0.72% of reference with a coverageData >= 3X There is a 0.54% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.37% of reference with a coverageData >= 6X There is a 0.33% of reference with a coverageData >= 7X There is a 0.31% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.28% of reference with a coverageData >= 10X There is a 0.27% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.25% of reference with a coverageData >= 13X There is a 0.24% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.23% of reference with a coverageData >= 16X There is a 0.22% of reference with a coverageData >= 17X There is a 0.21% of reference with a coverageData >= 18X There is a 0.21% of reference with a coverageData >= 19X There is a 0.2% of reference with a coverageData >= 20X There is a 0.2% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.19% of reference with a coverageData >= 23X There is a 0.19% of reference with a coverageData >= 24X There is a 0.18% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.17% of reference with a coverageData >= 28X There is a 0.17% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.17% of reference with a coverageData >= 31X There is a 0.16% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.16% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.15% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.15% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 251891979 1.0105971972683672 40.42901189111777 chr2 243199373 69925775 0.28752448716222634 11.048401247945238 chr3 198022430 143386586 0.7240926495044021 22.341534916253153 chr4 191154276 49115257 0.25694040451389116 14.978940517829578 chr5 180915260 76020979 0.4202021377301174 18.562886078351998 chr6 171115067 147290484 0.8607686428922124 43.74675267005209 chr7 159138663 96341727 0.6053948498989211 28.228971695450582 chr8 146364022 44690056 0.30533498184410374 10.77025366622563 chr9 141213431 70626707 0.5001415693950528 21.455677898437145 chr10 135534747 50637579 0.37361326243520415 16.99278914939168 chr11 135006516 56594409 0.41919761117307847 29.56825406192899 chr12 133851895 54610560 0.4079924307384666 13.973248747974187 chr13 115169878 26680268 0.23166012210241294 13.894331832413558 chr14 107349540 30362169 0.2828346446570707 14.3269657363042 chr15 102531392 47504469 0.4633163373028233 32.805968418329144 chr16 90354753 66688092 0.7380695512498385 36.24912328220643 chr17 81195210 64173226 0.79035728831787 26.520878296386233 chr18 78077248 21907026 0.28058143135372804 11.983696949903457 chr19 59128983 120647269 2.0404083222605065 112.00925595123395 chr20 63025520 27548675 0.4371034939497524 16.026742571157495 chr21 48129895 15809073 0.3284668084150194 28.910720442338146 chr22 51304566 20680811 0.4030988391949364 15.776884442932817 chrMT 16571 1852 0.11176151107356225 0.40447512359910354 chrX 155270560 42250692 0.2721101282818842 12.200031391885254 chrY 59373566 207114 0.0034883200379104734 0.17988456524300003