BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053610.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 = 7,458,168 number of mapped reads = 5,681,563 (76.18%) number of supplementary alignments = 185 (0%) number of secondary alignments = 0 number of mapped bases = 268,689,917 bp number of sequenced bases = 268,636,842 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,098,230 duplication rate = 15.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9453 >>>>>>> ACTG content number of A's = 78,386,966 bp (29.18%) number of C's = 51,641,452 bp (19.22%) number of T's = 81,410,237 bp (30.3%) number of G's = 57,075,287 bp (21.25%) number of N's = 122,900 bp (0.05%) GC percentage = 40.47% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,735,267 number of insertions = 12,306 mapped reads with insertion percentage = 0.22% number of deletions = 36,337 mapped reads with deletion percentage = 0.64% homopolymer indels = 48.22% >>>>>>> Coverage mean coverageData = 0.0868X std coverageData = 0.7387X There is a 4.67% of reference with a coverageData >= 1X There is a 1.78% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.46% of reference with a coverageData >= 4X There is a 0.27% of reference with a coverageData >= 5X There is a 0.17% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 21240198 0.08521622900991689 0.6571790965100379 chr2 243199373 22742051 0.09351196394737415 1.6703029994391276 chr3 198022430 18581951 0.09383760718419626 0.5685648086778292 chr4 191154276 17520406 0.09165584137913818 0.5897493169428518 chr5 180915260 16781167 0.09275705653575049 0.5629796576042345 chr6 171115067 16007047 0.09354551460976841 0.6334606560114066 chr7 159138663 14470315 0.09092897179863828 0.7222579746038261 chr8 146364022 13813835 0.09437999045967731 0.6171292288755068 chr9 141213431 11036108 0.07815197125264947 0.5452642752594733 chr10 135534747 12564619 0.09270404289757518 0.6398135246975606 chr11 135006516 12276745 0.09093446274844987 0.6237929659702803 chr12 133851895 12273423 0.09169405483575709 0.5620799908193872 chr13 115169878 8757516 0.07603998677501421 0.5103660612648063 chr14 107349540 8347036 0.07775567552501855 0.5659254255542634 chr15 102531392 7674387 0.07484914473803302 0.4944784841059349 chr16 90354753 7455193 0.08251024713663929 0.5532074563378937 chr17 81195210 6772075 0.0834048584885734 0.5297378087933985 chr18 78077248 7165423 0.09177350871793022 0.6861883405080655 chr19 59128983 4605853 0.07789501470032048 0.6255516669388301 chr20 63025520 5672814 0.09000820619964738 0.5729189693034709 chr21 48129895 3469341 0.07208287073969308 0.5648904010980861 chr22 51304566 2796237 0.05450269280126061 0.4047463506534569 chrMT 16571 33303 2.0097157685112546 3.5065523422290923 chrX 155270560 15959662 0.10278614310401148 0.6591774824646237 chrY 59373566 673212 0.011338581213060372 0.2312398267263823