BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054573.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 9,814,259 number of mapped reads = 7,116,760 (72.51%) number of supplementary alignments = 204 (0%) number of secondary alignments = 0 number of mapped bases = 336,917,770 bp number of sequenced bases = 336,848,868 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,022,007 duplication rate = 21.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7615 >>>>>>> ACTG content number of A's = 98,678,169 bp (29.29%) number of C's = 65,244,899 bp (19.37%) number of T's = 100,963,262 bp (29.97%) number of G's = 71,817,593 bp (21.32%) number of N's = 144,945 bp (0.04%) GC percentage = 40.69% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 2,056,831 number of insertions = 14,168 mapped reads with insertion percentage = 0.2% number of deletions = 45,617 mapped reads with deletion percentage = 0.64% homopolymer indels = 47.8% >>>>>>> Coverage mean coverageData = 0.1088X std coverageData = 0.8859X There is a 4.22% of reference with a coverageData >= 1X There is a 2.01% of reference with a coverageData >= 2X There is a 1.23% of reference with a coverageData >= 3X There is a 0.83% of reference with a coverageData >= 4X There is a 0.58% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.31% of reference with a coverageData >= 7X There is a 0.23% of reference with a coverageData >= 8X There is a 0.18% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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% 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 28863658 0.11580174959724573 0.981853089414702 chr2 243199373 31939619 0.13133100881802026 1.1445494333799588 chr3 198022430 22278949 0.11250719931070435 0.8486229561508923 chr4 191154276 16525459 0.08645089895870287 0.7254416600817342 chr5 180915260 17276026 0.09549236476790295 0.7653337597804366 chr6 171115067 21550280 0.12594028321304984 0.9432207326722595 chr7 159138663 17548288 0.11027042498151439 0.9071013363055703 chr8 146364022 18653169 0.1274436760148611 0.9420066604493088 chr9 141213431 17880786 0.12662241738181407 0.9453588257481406 chr10 135534747 11716838 0.08644896057540137 0.7842701189915257 chr11 135006516 16467985 0.12197918654533682 0.9303926427225834 chr12 133851895 17945845 0.13407240144041294 0.9398275282570469 chr13 115169878 8354045 0.07253671832490784 0.6689226186878953 chr14 107349540 6755830 0.06293301303387047 0.6831026442780708 chr15 102531392 10187520 0.09936000868885111 0.7772062194843954 chr16 90354753 8292817 0.09178063936492638 0.753889250883572 chr17 81195210 7847183 0.09664588588415499 0.7605401759216651 chr18 78077248 10613726 0.1359387820636301 1.049106920938987 chr19 59128983 6990730 0.11822848365242473 0.9310596221988662 chr20 63025520 7292140 0.11570138572438593 0.8322950974055433 chr21 48129895 3201111 0.06650982720822474 0.6538519688461274 chr22 51304566 5355641 0.10438916879250085 0.8043644074712816 chrMT 16571 12098 0.7300706052742744 1.8444986497631206 chrX 155270560 22581714 0.14543461426300003 1.021039302023607 chrY 59373566 786313 0.013243486166891172 0.24431032085522789