BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013187.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 = 2,942,938 number of mapped reads = 2,657,942 (90.32%) number of supplementary alignments = 25,615 (0.87%) number of secondary alignments = 0 number of mapped bases = 176,218,508 bp number of sequenced bases = 176,136,385 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 185,106 duplication rate = 4.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3939 >>>>>>> ACTG content number of A's = 48,080,747 bp (27.3%) number of C's = 33,003,218 bp (18.74%) number of T's = 54,916,268 bp (31.18%) number of G's = 40,115,616 bp (22.78%) number of N's = 20,536 bp (0.01%) GC percentage = 41.51% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,355,809 number of insertions = 13,389 mapped reads with insertion percentage = 0.5% number of deletions = 46,333 mapped reads with deletion percentage = 1.72% homopolymer indels = 45.94% >>>>>>> Coverage mean coverageData = 0.0569X std coverageData = 0.6442X There is a 4.12% of reference with a coverageData >= 1X There is a 0.98% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% 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 4804878 0.019277296003206348 0.4828822258392573 chr2 243199373 11275222 0.046362052092955026 0.826110329670032 chr3 198022430 5913439 0.02986247063022103 0.22560959581470463 chr4 191154276 12594936 0.06588885304349666 0.4335714795284438 chr5 180915260 3447818 0.019057640577140923 0.1886387068750001 chr6 171115067 10961729 0.06406057159186339 0.644987132713785 chr7 159138663 19240153 0.12090181378487515 1.4699001171792392 chr8 146364022 10843331 0.07408467498932217 0.6613023116078949 chr9 141213431 14845982 0.10513151542929369 0.7548239195678924 chr10 135534747 3643874 0.02688516473196353 0.5811884580075662 chr11 135006516 4667095 0.034569405524100774 0.4866505346543099 chr12 133851895 9119091 0.06812821738534221 0.3718069014360352 chr13 115169878 6598641 0.05729485100262067 0.31201101802719444 chr14 107349540 15590544 0.14523158646045434 0.5887798568422861 chr15 102531392 1686328 0.01644694339076173 0.18595513813465755 chr16 90354753 11050487 0.12230111458552712 0.5579747186641767 chr17 81195210 4500784 0.05543164430512588 0.34701672497561387 chr18 78077248 4318926 0.055316063394037655 1.4297486361122842 chr19 59128983 1848226 0.031257530676622666 0.7528860694151127 chr20 63025520 2603573 0.04130982179916961 0.3017092876777012 chr21 48129895 4792505 0.09957439134242865 0.5038575911030988 chr22 51304566 729357 0.014216220053396417 0.15165836994735607 chrMT 16571 83475 5.037414760726571 3.478535538835208 chrX 155270560 10662520 0.06867058378613435 0.5071292983247839 chrY 59373566 395594 0.006662796706534352 0.31273343293936506