BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514728.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 55,271,360 number of mapped reads = 52,939,086 (95.78%) number of supplementary alignments = 1,490,959 (2.7%) number of secondary alignments = 0 number of mapped bases = 5,037,763,825 bp number of sequenced bases = 5,035,373,112 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,586,234 duplication rate = 42.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2827 >>>>>>> ACTG content number of A's = 1,319,397,850 bp (26.2%) number of C's = 1,174,006,985 bp (23.32%) number of T's = 1,334,724,735 bp (26.51%) number of G's = 1,177,098,374 bp (23.38%) number of N's = 30,145,168 bp (0.6%) GC percentage = 46.69% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 40,988,851 number of insertions = 1,731,620 mapped reads with insertion percentage = 3.17% number of deletions = 1,285,805 mapped reads with deletion percentage = 2.36% homopolymer indels = 45.25% >>>>>>> Coverage mean coverageData = 1.6273X std coverageData = 59.587X There is a 5.43% of reference with a coverageData >= 1X There is a 3.41% of reference with a coverageData >= 2X There is a 2.68% of reference with a coverageData >= 3X There is a 2.32% of reference with a coverageData >= 4X There is a 2.09% of reference with a coverageData >= 5X There is a 1.91% of reference with a coverageData >= 6X There is a 1.78% of reference with a coverageData >= 7X There is a 1.66% of reference with a coverageData >= 8X There is a 1.57% of reference with a coverageData >= 9X There is a 1.48% of reference with a coverageData >= 10X There is a 1.41% of reference with a coverageData >= 11X There is a 1.34% of reference with a coverageData >= 12X There is a 1.29% of reference with a coverageData >= 13X There is a 1.23% of reference with a coverageData >= 14X There is a 1.18% of reference with a coverageData >= 15X There is a 1.14% of reference with a coverageData >= 16X There is a 1.1% of reference with a coverageData >= 17X There is a 1.06% of reference with a coverageData >= 18X There is a 1.03% of reference with a coverageData >= 19X There is a 0.99% of reference with a coverageData >= 20X There is a 0.96% of reference with a coverageData >= 21X There is a 0.94% of reference with a coverageData >= 22X There is a 0.91% of reference with a coverageData >= 23X There is a 0.88% of reference with a coverageData >= 24X There is a 0.86% of reference with a coverageData >= 25X There is a 0.84% of reference with a coverageData >= 26X There is a 0.82% of reference with a coverageData >= 27X There is a 0.8% of reference with a coverageData >= 28X There is a 0.78% of reference with a coverageData >= 29X There is a 0.76% of reference with a coverageData >= 30X There is a 0.74% of reference with a coverageData >= 31X There is a 0.72% of reference with a coverageData >= 32X There is a 0.71% of reference with a coverageData >= 33X There is a 0.69% of reference with a coverageData >= 34X There is a 0.68% of reference with a coverageData >= 35X There is a 0.67% of reference with a coverageData >= 36X There is a 0.65% of reference with a coverageData >= 37X There is a 0.64% of reference with a coverageData >= 38X There is a 0.63% of reference with a coverageData >= 39X There is a 0.62% of reference with a coverageData >= 40X There is a 0.6% of reference with a coverageData >= 41X There is a 0.59% of reference with a coverageData >= 42X There is a 0.58% of reference with a coverageData >= 43X There is a 0.57% of reference with a coverageData >= 44X There is a 0.56% of reference with a coverageData >= 45X There is a 0.55% of reference with a coverageData >= 46X There is a 0.54% of reference with a coverageData >= 47X There is a 0.53% of reference with a coverageData >= 48X There is a 0.53% of reference with a coverageData >= 49X There is a 0.52% of reference with a coverageData >= 50X There is a 0.51% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 168344606 0.6754029551645531 11.779882938575284 chr2 243199373 262300605 1.0785414524896821 22.29494451669328 chr3 198022430 774103329 3.909169930901262 84.16651480408987 chr4 191154276 66061101 0.3455904957103863 6.606248889191335 chr5 180915260 208364756 1.1517257084891568 23.6746581597826 chr6 171115067 271012470 1.58380249472713 29.48760199934767 chr7 159138663 821859146 5.164421583710301 64.42208471378062 chr8 146364022 53952792 0.36862058901333006 8.932428607650005 chr9 141213431 346527596 2.45392802615213 215.96863395516394 chr10 135534747 78654817 0.5803295371924072 21.31178502286586 chr11 135006516 580627421 4.300736277054954 88.85570912293514 chr12 133851895 284933527 2.128722398737799 38.13119627451849 chr13 115169878 54287261 0.47136683604023616 13.281138993764232 chr14 107349540 192432912 1.792582548560525 29.12457990789776 chr15 102531392 166417683 1.6230900581160548 29.058989259521574 chr16 90354753 220127600 2.4362592192576744 45.47291663335351 chr17 81195210 86991658 1.071389038836158 13.935287157237797 chr18 78077248 47149183 0.60387864848925 29.031301841203874 chr19 59128983 74769396 1.2645134789482173 27.29342340441794 chr20 63025520 61258825 0.9719685771731832 19.04721550750737 chr21 48129895 25983273 0.5398572550386823 8.192112581809756 chr22 51304566 70971743 1.3833416503318632 13.362930171460995 chrMT 16571 4566159 275.55120391044596 127.82757221715919 chrX 155270560 110660959 0.7126976227818075 15.522808353417279 chrY 59373566 5405007 0.09103389545441821 7.795106608503684