BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779398.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 14,004,464 number of mapped reads = 13,450,221 (96.04%) number of supplementary alignments = 44,177 (0.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,763,385 number of mapped paired reads (second in pair) = 6,686,836 number of mapped paired reads (both in pair) = 13,346,644 number of mapped paired reads (singletons) = 103,577 number of mapped bases = 1,068,995,312 bp number of sequenced bases = 1,068,761,666 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 430,254 duplication rate = 2.75% >>>>>>> Insert size mean insert size = 73,613.1631 std insert size = 2,602,703.9663 median insert size = 178 >>>>>>> Mapping quality mean mapping quality = 53.3114 >>>>>>> ACTG content number of A's = 319,734,823 bp (29.92%) number of C's = 214,151,266 bp (20.04%) number of T's = 316,436,767 bp (29.61%) number of G's = 218,199,455 bp (20.42%) number of N's = 239,355 bp (0.02%) GC percentage = 40.45% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 3,463,386 number of insertions = 94,236 mapped reads with insertion percentage = 0.69% number of deletions = 112,280 mapped reads with deletion percentage = 0.82% homopolymer indels = 47.14% >>>>>>> Coverage mean coverageData = 0.3453X std coverageData = 1.4071X There is a 21.3% of reference with a coverageData >= 1X There is a 7.57% of reference with a coverageData >= 2X There is a 2.69% of reference with a coverageData >= 3X There is a 1.06% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.24% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 79226921 0.3178604758621644 2.7441718419622716 chr2 243199373 86410244 0.35530619562904875 0.8603396227570936 chr3 198022430 78546234 0.39665321751682375 0.8117045820511234 chr4 191154276 61885411 0.3237458888965685 0.7470699501467891 chr5 180915260 105005837 0.5804144824488547 1.0091429749633938 chr6 171115067 47472548 0.2774305549610076 0.9024107362451906 chr7 159138663 137769742 0.8657213740698576 3.401656691662843 chr8 146364022 48716142 0.3328423292439996 0.7799208728126037 chr9 141213431 55210212 0.3909699779194516 1.4450460947175463 chr10 135534747 21175024 0.156233176131579 1.588796983900787 chr11 135006516 45752341 0.33888987254511477 0.8135640594177294 chr12 133851895 48130926 0.3595834485570787 0.7859186565106278 chr13 115169878 35487545 0.3081321749772106 0.727265415092993 chr14 107349540 33806387 0.3149187877283871 0.7365417890073288 chr15 102531392 22422464 0.21868876997202963 0.623271812815487 chr16 90354753 29581868 0.3273969217756591 0.7829473596569009 chr17 81195210 19857391 0.24456357708786022 0.8436830841104078 chr18 78077248 25962682 0.332525577745773 1.0945478759487537 chr19 59128983 13902875 0.23512792364448412 1.8445492755806263 chr20 63025520 15355613 0.24364119486836444 0.6435769646480741 chr21 48129895 12085705 0.25110599140097856 0.675406621111399 chr22 51304566 10263145 0.20004350100145082 0.6296743860000997 chrMT 16571 720 0.04344939955343673 0.223898942306641 chrX 155270560 29916820 0.19267541767093518 0.590821926772691 chrY 59373566 5050515 0.08506335967760467 0.40007338845424073