BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063576.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 = 3,275,471 number of mapped reads = 3,039,824 (92.81%) number of supplementary alignments = 14,952 (0.46%) number of secondary alignments = 0 number of mapped bases = 204,116,909 bp number of sequenced bases = 204,033,772 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 174,710 duplication rate = 4.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1803 >>>>>>> ACTG content number of A's = 57,301,760 bp (28.08%) number of C's = 37,946,036 bp (18.6%) number of T's = 64,211,552 bp (31.47%) number of G's = 44,568,775 bp (21.84%) number of N's = 5,649 bp (0%) GC percentage = 40.44% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 1,455,240 number of insertions = 13,893 mapped reads with insertion percentage = 0.45% number of deletions = 47,768 mapped reads with deletion percentage = 1.56% homopolymer indels = 48.12% >>>>>>> Coverage mean coverageData = 0.0659X std coverageData = 0.5859X There is a 4.98% of reference with a coverageData >= 1X There is a 1.08% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% 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% of reference with a coverageData >= 9X There is a 0% 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 26477714 0.10622927996636766 0.8623753482914971 chr2 243199373 21917572 0.09012182774007399 0.8842692062931539 chr3 198022430 3834141 0.01936215508515879 0.23874288591220474 chr4 191154276 11355778 0.059406350920447104 0.31884504885819337 chr5 180915260 8533459 0.04716826540779368 0.2683858855147412 chr6 171115067 6897682 0.04031019664679791 0.26549353378252455 chr7 159138663 19078218 0.11988424208389888 1.02661122245827 chr8 146364022 10738026 0.0733652017296983 0.5780712498804182 chr9 141213431 6538343 0.04630114114287047 0.5668431533658761 chr10 135534747 9862392 0.07276652089814283 0.8705274668304896 chr11 135006516 11012624 0.08157105542965053 0.4768337576530214 chr12 133851895 8103454 0.06054045032384487 0.3245551460900438 chr13 115169878 3517767 0.030544158430036716 0.21407833569773974 chr14 107349540 3281190 0.030565477970376027 0.28492874522630346 chr15 102531392 2760528 0.026923734732870887 0.20395018095448253 chr16 90354753 5083515 0.05626173312653514 0.35774003265591825 chr17 81195210 3642268 0.044858163431069395 0.34990514383057136 chr18 78077248 10635672 0.13621986266729072 0.9421342879094711 chr19 59128983 2272216 0.03842812584819867 0.7470536805182451 chr20 63025520 965828 0.015324395578172143 0.1867530225477962 chr21 48129895 2814874 0.058484939557836145 0.3259478518699936 chr22 51304566 1471130 0.028674445857314143 0.20697358030834967 chrMT 16571 80055 4.831030112847746 3.9977821852587456 chrX 155270560 22793936 0.14680140266126432 0.6415190131432281 chrY 59373566 448527 0.0075543213961580145 0.16935978343537483