BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971316.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,503,271 number of mapped reads = 9,454,411 (90.01%) number of supplementary alignments = 1,264 (0.01%) number of secondary alignments = 0 number of mapped bases = 453,144,503 bp number of sequenced bases = 453,046,502 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 927,584 duplication rate = 8.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.6089 >>>>>>> ACTG content number of A's = 129,446,943 bp (28.57%) number of C's = 93,983,153 bp (20.74%) number of T's = 132,590,037 bp (29.27%) number of G's = 97,000,502 bp (21.41%) number of N's = 25,867 bp (0.01%) GC percentage = 42.16% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 2,060,525 number of insertions = 27,822 mapped reads with insertion percentage = 0.29% number of deletions = 66,752 mapped reads with deletion percentage = 0.7% homopolymer indels = 42.48% >>>>>>> Coverage mean coverageData = 0.1464X std coverageData = 1.1273X There is a 9.37% of reference with a coverageData >= 1X There is a 3.09% of reference with a coverageData >= 2X There is a 1.11% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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% 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 36559326 0.14667697056610343 1.8901830915777005 chr2 243199373 38324900 0.15758634377729255 1.0277979534336688 chr3 198022430 31761766 0.16039478962054954 0.587944342510113 chr4 191154276 30261706 0.1583103796223737 0.6908419458277063 chr5 180915260 28286005 0.15634946991204612 0.5772858690104372 chr6 171115067 26995463 0.15776204558304618 0.6275213709498625 chr7 159138663 25979227 0.16324899625429176 1.6227774560008044 chr8 146364022 23589043 0.16116694989428482 2.3826900091155725 chr9 141213431 18706072 0.13246666317455313 0.9539399022154129 chr10 135534747 21667172 0.15986433353507495 1.220844842569588 chr11 135006516 20785049 0.15395589498806117 0.8868063331008156 chr12 133851895 20782872 0.15526767103297268 0.5960415931828152 chr13 115169878 14888839 0.1292771969420685 0.5269522799566327 chr14 107349540 13873564 0.1292372934248251 0.6496839047223677 chr15 102531392 13196361 0.12870556755925053 0.5139747831744285 chr16 90354753 12480812 0.13813121707056186 0.6556669103665744 chr17 81195210 11558702 0.14235694445522093 0.6852875475738265 chr18 78077248 14646424 0.18758888632960014 1.8894884722841798 chr19 59128983 9484349 0.16040101687526065 1.659273566685295 chr20 63025520 8920905 0.14154432997934804 0.5738986527615195 chr21 48129895 6109401 0.12693568103566402 0.6849271405203577 chr22 51304566 4604780 0.0897538047588201 0.5212758898195571 chrMT 16571 161955 9.773399312051174 7.601355117715385 chrX 155270560 15618487 0.10058884955396567 0.5978547697854655 chrY 59373566 3901323 0.06570807958545054 0.6583480345099222