BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240071.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 = 1,568,199 number of mapped reads = 1,126,585 (71.84%) number of supplementary alignments = 5,325 (0.34%) number of secondary alignments = 0 number of mapped bases = 69,695,814 bp number of sequenced bases = 69,657,449 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 231,896 duplication rate = 14.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7559 >>>>>>> ACTG content number of A's = 18,532,718 bp (26.61%) number of C's = 11,922,826 bp (17.12%) number of T's = 23,319,076 bp (33.48%) number of G's = 15,877,282 bp (22.79%) number of N's = 5,547 bp (0.01%) GC percentage = 39.91% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 669,342 number of insertions = 5,027 mapped reads with insertion percentage = 0.44% number of deletions = 22,380 mapped reads with deletion percentage = 1.97% homopolymer indels = 49.6% >>>>>>> Coverage mean coverageData = 0.0225X std coverageData = 0.3112X There is a 1.08% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% 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 5826964 0.023377931724390767 0.4014461381560642 chr2 243199373 6811069 0.02800611249931142 0.36162215690909216 chr3 198022430 6310422 0.03186720817434671 0.3352021947375607 chr4 191154276 4167951 0.021804121190571745 0.27895032422599636 chr5 180915260 3971405 0.02195174138433651 0.27727058235880275 chr6 171115067 4577335 0.026750040661235285 0.3259732934507597 chr7 159138663 4268820 0.02682453100664796 0.3540450998580371 chr8 146364022 3795881 0.025934522351401357 0.40929762690001625 chr9 141213431 3205826 0.02270199071928222 0.3042712969093802 chr10 135534747 3082652 0.022744366800640427 0.30397780562563614 chr11 135006516 2292961 0.01698407653153571 0.255062194922391 chr12 133851895 3076868 0.022987108251250384 0.2808153631141191 chr13 115169878 1929461 0.016753173950570653 0.24251118473749056 chr14 107349540 2391189 0.022274795029396492 0.2820399292980404 chr15 102531392 1920856 0.018734320899495834 0.2558697619765751 chr16 90354753 1880203 0.0208091211316797 0.25532187268070183 chr17 81195210 1343963 0.016552244892278745 0.23078827054472015 chr18 78077248 1461529 0.01871901273979329 0.36051685728199484 chr19 59128983 1059967 0.01792635263150053 0.2782855049308616 chr20 63025520 1372773 0.021781224494458754 0.278711342097619 chr21 48129895 850880 0.017678825187547157 0.25681376550330853 chr22 51304566 726514 0.014160805882267867 0.21049231562260282 chrMT 16571 39055 2.356828193832599 3.318836643611121 chrX 155270560 3176606 0.02045852091987045 0.26877608705605716 chrY 59373566 154664 0.002604930281600401 0.08224630093747726