BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927064.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 32,137,772 number of mapped reads = 31,660,072 (98.51%) number of supplementary alignments = 361,630 (1.13%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,893,624 number of mapped paired reads (second in pair) = 15,766,448 number of mapped paired reads (both in pair) = 31,372,028 number of mapped paired reads (singletons) = 288,044 number of mapped bases = 3,014,775,601 bp number of sequenced bases = 3,012,526,397 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,082,023 duplication rate = 5.19% >>>>>>> Insert size mean insert size = 117,760.8471 std insert size = 3,354,700.783 median insert size = 191 >>>>>>> Mapping quality mean mapping quality = 53.5927 >>>>>>> ACTG content number of A's = 872,018,985 bp (28.95%) number of C's = 599,570,472 bp (19.9%) number of T's = 882,038,270 bp (29.28%) number of G's = 658,382,162 bp (21.85%) number of N's = 516,508 bp (0.02%) GC percentage = 41.76% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 30,845,861 number of insertions = 487,015 mapped reads with insertion percentage = 1.51% number of deletions = 1,603,255 mapped reads with deletion percentage = 4.93% homopolymer indels = 53.06% >>>>>>> Coverage mean coverageData = 0.9739X std coverageData = 3.5989X There is a 35.38% of reference with a coverageData >= 1X There is a 21% of reference with a coverageData >= 2X There is a 12.88% of reference with a coverageData >= 3X There is a 8.32% of reference with a coverageData >= 4X There is a 5.52% of reference with a coverageData >= 5X There is a 3.74% of reference with a coverageData >= 6X There is a 2.59% of reference with a coverageData >= 7X There is a 1.81% of reference with a coverageData >= 8X There is a 1.29% of reference with a coverageData >= 9X There is a 0.92% of reference with a coverageData >= 10X There is a 0.67% of reference with a coverageData >= 11X There is a 0.49% of reference with a coverageData >= 12X There is a 0.36% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 240982388 0.966827633300059 4.5921675663036385 chr2 243199373 265840502 1.0930969875485657 5.984769343000783 chr3 198022430 205327474 1.0368899826145956 2.031709552342195 chr4 191154276 184207273 0.963657611300309 2.7267677460085173 chr5 180915260 186238958 1.0294264729243956 1.9979707184082838 chr6 171115067 178263110 1.041773311522591 2.032462878074139 chr7 159138663 149948250 0.9422490246760462 2.683756328085794 chr8 146364022 155355728 1.0614338542842174 2.4722102251686797 chr9 141213431 129836463 0.9194342356854144 5.065387927769447 chr10 135534747 147260550 1.0865151059750013 6.775213227326604 chr11 135006516 144559375 1.0707585032414286 3.6598970745499706 chr12 133851895 136624924 1.0207171441241083 2.018787472063416 chr13 115169878 88222156 0.7660176213783955 1.7141558499739855 chr14 107349540 93106717 0.8673229247186341 1.9269625056636397 chr15 102531392 89864110 0.8764545984121624 1.9536181664021295 chr16 90354753 92177233 1.0201702726142143 4.326286938601803 chr17 81195210 77654416 0.9563915900950315 3.0305092957581716 chr18 78077248 81915475 1.0491593530550667 5.24181911915135 chr19 59128983 43356740 0.7332569883706608 2.8926860937672676 chr20 63025520 69301349 1.09957599715163 2.296493034590108 chr21 48129895 38010301 0.7897441081057833 2.3401838626233693 chr22 51304566 34692560 0.6762080396508958 1.7760046480119813 chrMT 16571 225038 13.580230523203186 10.463760237345074 chrX 155270560 177247729 1.1415411202226617 2.4642977371163224 chrY 59373566 4556782 0.0767476556823284 1.9718498755966505