BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238649.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 = 2,956,425 number of mapped reads = 2,540,861 (85.94%) number of supplementary alignments = 22,098 (0.75%) number of secondary alignments = 0 number of mapped bases = 154,068,830 bp number of sequenced bases = 153,994,087 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,025,440 duplication rate = 21.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.4609 >>>>>>> ACTG content number of A's = 36,946,999 bp (23.99%) number of C's = 27,088,483 bp (17.59%) number of T's = 52,316,251 bp (33.97%) number of G's = 37,639,044 bp (24.44%) number of N's = 3,310 bp (0%) GC percentage = 42.03% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 915,785 number of insertions = 10,268 mapped reads with insertion percentage = 0.4% number of deletions = 44,705 mapped reads with deletion percentage = 1.75% homopolymer indels = 40.35% >>>>>>> Coverage mean coverageData = 0.0498X std coverageData = 1.1339X There is a 1.48% of reference with a coverageData >= 1X There is a 0.79% of reference with a coverageData >= 2X There is a 0.58% of reference with a coverageData >= 3X There is a 0.45% of reference with a coverageData >= 4X There is a 0.35% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.21% of reference with a coverageData >= 7X There is a 0.16% of reference with a coverageData >= 8X There is a 0.13% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 4718279 0.018929858553893033 1.0567410387218115 chr2 243199373 11616750 0.04776636492397536 2.600972208205355 chr3 198022430 31976106 0.161477192255443 1.1504076728571144 chr4 191154276 11429896 0.05979409008878253 0.6574176108726895 chr5 180915260 3891064 0.021507660547816696 0.39268853932702485 chr6 171115067 13426870 0.07846690671605207 1.1296102552412557 chr7 159138663 9929118 0.06239287054962878 1.2667000587214348 chr8 146364022 5112913 0.03493285392225693 1.4637509570734468 chr9 141213431 6865978 0.04862128163998791 0.6722982816002491 chr10 135534747 3504395 0.025856063316368607 0.4417683876717473 chr11 135006516 3340584 0.024743872362427307 0.440297931963941 chr12 133851895 2257187 0.016863317474885207 0.3601911842937072 chr13 115169878 917629 0.007967612850992166 0.5733313200788255 chr14 107349540 2034557 0.01895263826933958 0.4133591155311269 chr15 102531392 4524716 0.04413005531028 0.7554737163894348 chr16 90354753 2449941 0.027114688698224875 0.46427389530973023 chr17 81195210 7841588 0.09657697787837484 0.8970843856895162 chr18 78077248 9250603 0.11848013649251572 2.222310385985107 chr19 59128983 8279066 0.14001705390400507 1.195760115773849 chr20 63025520 1567265 0.024867149053272388 0.4306675904759101 chr21 48129895 3608841 0.0749812772290486 0.782671004161402 chr22 51304566 3306735 0.06445303523277052 0.7130909062191587 chrMT 16571 36714 2.215557298895661 3.9618351977970128 chrX 155270560 1935569 0.012465782309280008 0.29974863849164174 chrY 59373566 246466 0.004151106571567556 0.3365101669974175