BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472821.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 2,084,914 number of mapped reads = 1,193,967 (57.27%) number of supplementary alignments = 8,826 (0.42%) number of secondary alignments = 0 number of mapped bases = 72,540,768 bp number of sequenced bases = 72,500,241 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,331 duplication rate = 7.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9142 >>>>>>> ACTG content number of A's = 19,917,477 bp (27.47%) number of C's = 13,862,024 bp (19.12%) number of T's = 21,690,464 bp (29.92%) number of G's = 17,029,006 bp (23.49%) number of N's = 1,270 bp (0%) GC percentage = 42.61% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 698,289 number of insertions = 5,621 mapped reads with insertion percentage = 0.47% number of deletions = 22,567 mapped reads with deletion percentage = 1.87% homopolymer indels = 47.68% >>>>>>> Coverage mean coverageData = 0.0234X std coverageData = 0.2713X There is a 1.58% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 5743730 0.023043994742945897 0.30593776277330653 chr2 243199373 6112371 0.025133169237241414 0.30274475872010187 chr3 198022430 5119084 0.02585103111804052 0.23779592884700954 chr4 191154276 3882842 0.02031260864915206 0.22578144658698113 chr5 180915260 4144286 0.02290733241629258 0.2312981696202763 chr6 171115067 4586683 0.026804670567086884 0.2609077042330736 chr7 159138663 4217850 0.0265042442891455 0.38677719439515346 chr8 146364022 3562208 0.024338002955398425 0.27771789240422945 chr9 141213431 3201361 0.02267037191384437 0.2761793779590964 chr10 135534747 3516791 0.025947523257633706 0.26341865828208255 chr11 135006516 3008645 0.022285183627729493 0.2708852630074175 chr12 133851895 3525168 0.02633633240679932 0.25533518091967344 chr13 115169878 2432269 0.02111896827745185 0.225427954293419 chr14 107349540 2488610 0.02318230706903821 0.2541300442510877 chr15 102531392 2237295 0.021820585445675018 0.24975731908773013 chr16 90354753 2076188 0.0229781824537775 0.24000557714155685 chr17 81195210 1837035 0.02262491839112184 0.24234562233563398 chr18 78077248 1563516 0.020025244742232717 0.3637143479074887 chr19 59128983 1398095 0.02364483420930815 0.27473858289572084 chr20 63025520 1710708 0.02714310012832897 0.2601203672434884 chr21 48129895 1002454 0.02082809447226095 0.22750722778021587 chr22 51304566 867857 0.016915784844569196 0.2017198840539264 chrMT 16571 151962 9.170357854082432 6.9555012405378465 chrX 155270560 3922164 0.025260190985335534 0.2599799615810685 chrY 59373566 231596 0.0039006584175860348 0.09580903456909409