BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231730.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,096,206 number of mapped reads = 3,552,061 (86.72%) number of supplementary alignments = 35,706 (0.87%) number of secondary alignments = 0 number of mapped bases = 244,596,455 bp number of sequenced bases = 244,523,596 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 839,608 duplication rate = 9.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9554 >>>>>>> ACTG content number of A's = 59,948,947 bp (24.52%) number of C's = 41,037,343 bp (16.78%) number of T's = 64,646,410 bp (26.44%) number of G's = 78,837,810 bp (32.24%) number of N's = 53,086 bp (0.02%) GC percentage = 49.02% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,364,096 number of insertions = 14,029 mapped reads with insertion percentage = 0.39% number of deletions = 45,511 mapped reads with deletion percentage = 1.27% homopolymer indels = 47.46% >>>>>>> Coverage mean coverageData = 0.079X std coverageData = 65.9568X There is a 2.76% of reference with a coverageData >= 1X There is a 1.52% of reference with a coverageData >= 2X There is a 0.9% of reference with a coverageData >= 3X There is a 0.54% of reference with a coverageData >= 4X There is a 0.34% of reference with a coverageData >= 5X There is a 0.22% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% 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 0.01% 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 10404408 0.041742756580734855 0.9247537876200901 chr2 243199373 61023884 0.25092122256417165 235.30682947556497 chr3 198022430 10177679 0.051396596840065034 0.45448545537208773 chr4 191154276 7965526 0.04167066605405154 0.39593148233604175 chr5 180915260 8390238 0.046376618534003156 0.4245560429584325 chr6 171115067 51734660 0.302338425873392 1.326260582732157 chr7 159138663 3549870 0.022306772804796027 0.3863676808142774 chr8 146364022 38308882 0.26173701348545886 1.3369497766263827 chr9 141213431 3665095 0.02595429467328784 0.3301740085763897 chr10 135534747 6852811 0.050561285217878484 0.48806759894403956 chr11 135006516 14670498 0.10866511065288138 1.401211162639078 chr12 133851895 2793232 0.02086807960395331 0.29315887730963397 chr13 115169878 4099553 0.035595704981123626 0.38647124235228025 chr14 107349540 2960784 0.027580779572972555 0.4404219691918156 chr15 102531392 2050427 0.01999804118527914 0.30318055039996666 chr16 90354753 1647887 0.018237966961184654 0.26944338656578104 chr17 81195210 1736733 0.021389599214042307 0.5729025311891608 chr18 78077248 1628806 0.020861467863211573 0.34133063858471635 chr19 59128983 1853170 0.03134114449423221 0.6305248551831714 chr20 63025520 2391528 0.03794539100986394 0.39964903643277155 chr21 48129895 942184 0.01957585820621466 0.2889089244300052 chr22 51304566 647468 0.012620085315603293 0.21176122542240133 chrMT 16571 32529 1.96300766399131 3.1923626099193285 chrX 155270560 4719666 0.0303963996780845 0.4212199394021325 chrY 59373566 348937 0.005876975622451244 0.13318506892532073