BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004015.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 = 2,005,535 number of mapped reads = 1,831,658 (91.33%) number of supplementary alignments = 12,164 (0.61%) number of secondary alignments = 0 number of mapped bases = 123,699,206 bp number of sequenced bases = 123,648,312 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,377 duplication rate = 3.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6841 >>>>>>> ACTG content number of A's = 34,971,759 bp (28.28%) number of C's = 23,049,907 bp (18.64%) number of T's = 39,034,023 bp (31.57%) number of G's = 26,570,762 bp (21.49%) number of N's = 21,861 bp (0.02%) GC percentage = 40.13% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,038,968 number of insertions = 8,889 mapped reads with insertion percentage = 0.48% number of deletions = 28,813 mapped reads with deletion percentage = 1.55% homopolymer indels = 47.2% >>>>>>> Coverage mean coverageData = 0.04X std coverageData = 0.3142X There is a 3.3% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.1% 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% of reference with a coverageData >= 6X There is a 0% 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 8035426 0.03223833893677641 0.38637453489031837 chr2 243199373 8542256 0.03512449845008441 0.3249328228220255 chr3 198022430 10285508 0.05194112606334545 0.266158748486293 chr4 191154276 8291169 0.04337422721320657 0.25981616934717155 chr5 180915260 7427005 0.041052396575059505 0.236776353792691 chr6 171115067 6697397 0.03913972695344239 0.2442033243290994 chr7 159138663 7369154 0.04630649686933715 0.5145484357224333 chr8 146364022 8017528 0.054777997286792245 0.5213290567591037 chr9 141213431 5571498 0.03945444821038305 0.29677690981192384 chr10 135534747 5712103 0.04214493424331991 0.3247893114879578 chr11 135006516 4427781 0.03279679478581612 0.24099023596027594 chr12 133851895 6902295 0.05156665880598851 0.2698497767727961 chr13 115169878 3267295 0.028369353660338166 0.2020838236928853 chr14 107349540 2568795 0.023929259501251705 0.19257187608908474 chr15 102531392 5956713 0.05809648034428324 0.2846570971206801 chr16 90354753 3928973 0.04348385524334287 0.2544702060177567 chr17 81195210 2197358 0.0270626555433504 0.1969092975677876 chr18 78077248 3095487 0.03964646653529592 0.45482532292799804 chr19 59128983 2184957 0.03695238593905801 0.318121212294551 chr20 63025520 2913393 0.04622560829327549 0.25808765232178044 chr21 48129895 1454903 0.03022867596116717 0.22487196601174808 chr22 51304566 926278 0.018054494408938183 0.15272339573451174 chrMT 16571 32263 1.946955524711846 2.0441164210628244 chrX 155270560 7618098 0.04906337685650132 0.2772741301668014 chrY 59373566 275573 0.004641341569411546 0.1144706443024036