BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237245.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 = 3,051,947 number of mapped reads = 2,846,671 (93.27%) number of supplementary alignments = 22,273 (0.73%) number of secondary alignments = 0 number of mapped bases = 201,462,747 bp number of sequenced bases = 201,375,064 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,103 duplication rate = 3.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4748 >>>>>>> ACTG content number of A's = 58,560,659 bp (29.08%) number of C's = 38,924,315 bp (19.33%) number of T's = 61,910,050 bp (30.74%) number of G's = 41,976,461 bp (20.84%) number of N's = 3,579 bp (0%) GC percentage = 40.17% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,512,749 number of insertions = 15,600 mapped reads with insertion percentage = 0.54% number of deletions = 52,346 mapped reads with deletion percentage = 1.82% homopolymer indels = 48.32% >>>>>>> Coverage mean coverageData = 0.0651X std coverageData = 0.6889X There is a 4.43% of reference with a coverageData >= 1X There is a 1.32% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% 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% 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 24949558 0.10009827819044832 1.2347644115281053 chr2 243199373 18986489 0.07806964617462234 0.49444132246026523 chr3 198022430 9097575 0.04594214402883552 0.2904516166802682 chr4 191154276 18005535 0.09419373386133408 0.432492674457679 chr5 180915260 10522382 0.058161937251727684 0.33035265193230257 chr6 171115067 15826951 0.09249302985107676 0.42162574909724 chr7 159138663 5531074 0.03475631814249941 0.2743323438610265 chr8 146364022 6816325 0.046571041891702046 2.0240801856816653 chr9 141213431 9348321 0.06619994241199338 0.48260395721227684 chr10 135534747 3870758 0.02855915612547681 0.3637393226821164 chr11 135006516 4876265 0.036118738150386756 0.30013934204244047 chr12 133851895 3311643 0.024741099108085095 0.22804958110724388 chr13 115169878 12237863 0.10625923385974238 0.4626034467776611 chr14 107349540 9406865 0.08762836803958358 0.41606249899029957 chr15 102531392 6026801 0.058780056355813445 0.32370798636199266 chr16 90354753 6609504 0.07315059563053644 0.38113401380423984 chr17 81195210 6283488 0.07738742223833155 0.4892484019182871 chr18 78077248 1173828 0.015034187680385456 0.6896763186363513 chr19 59128983 3747102 0.06337166326706482 0.9931628127775988 chr20 63025520 6049426 0.09598375388255424 0.4430197289035047 chr21 48129895 1536280 0.0319194546341728 0.25547459149006746 chr22 51304566 3589615 0.06996677449722506 0.35557917304068737 chrMT 16571 296010 17.863134391406675 10.75820872565395 chrX 155270560 12976571 0.0835739305635273 0.44432011714724895 chrY 59373566 386518 0.006509934067291831 0.16530797654576282