BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013308.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 = 2,753,875 number of mapped reads = 2,485,484 (90.25%) number of supplementary alignments = 17,331 (0.63%) number of secondary alignments = 0 number of mapped bases = 161,542,810 bp number of sequenced bases = 161,473,746 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,477 duplication rate = 2.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0436 >>>>>>> ACTG content number of A's = 44,507,520 bp (27.56%) number of C's = 30,822,767 bp (19.09%) number of T's = 49,222,408 bp (30.48%) number of G's = 36,882,440 bp (22.84%) number of N's = 38,611 bp (0.02%) GC percentage = 41.93% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,285,744 number of insertions = 11,428 mapped reads with insertion percentage = 0.45% number of deletions = 39,913 mapped reads with deletion percentage = 1.59% homopolymer indels = 44.81% >>>>>>> Coverage mean coverageData = 0.0522X std coverageData = 0.4809X There is a 4.55% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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% 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 13327813 0.05347153377804423 1.0073266922088089 chr2 243199373 15638061 0.06430140344152943 0.5667150808446372 chr3 198022430 10943887 0.055265895888662715 0.2628236656563177 chr4 191154276 10833675 0.05667503352109162 0.27545907871922143 chr5 180915260 9925316 0.054861684967868384 0.2611833928382158 chr6 171115067 8040535 0.046989053278400084 0.3255129203571417 chr7 159138663 8407446 0.05283094529957186 0.668193078084187 chr8 146364022 7938229 0.05423620430436108 0.4741203155582437 chr9 141213431 5979443 0.042343302316618876 0.39735262586106923 chr10 135534747 7457052 0.055019485150918535 0.5264392154127039 chr11 135006516 6254741 0.046329178659791505 0.32760241640363164 chr12 133851895 8265701 0.061752588560662514 0.282319272729011 chr13 115169878 3592340 0.031191662806137554 0.19721618832295135 chr14 107349540 4706903 0.04384651298924988 0.2619121713541014 chr15 102531392 4212289 0.041082920243587444 0.22790006280520167 chr16 90354753 5125835 0.0567301091509818 0.2991784492710078 chr17 81195210 4230898 0.052107729015049044 0.28848713281239213 chr18 78077248 4128693 0.052879591760201385 0.6864188655484993 chr19 59128983 3306468 0.05591958177261395 0.7804055272419024 chr20 63025520 4510020 0.07155863212235297 0.3067898293700657 chr21 48129895 2619479 0.05442519664753061 0.2803519012243168 chr22 51304566 1637204 0.031911467684961996 0.19598764463594714 chrMT 16571 180551 10.895600748295214 7.295429789760271 chrX 155270560 9886969 0.06367574767554132 0.3273115800618755 chrY 59373566 393262 0.006623519968465428 0.13437847575905695