BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779308.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 = 17,536,992 number of mapped reads = 16,546,035 (94.35%) number of supplementary alignments = 42,460 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,395,466 number of mapped paired reads (second in pair) = 8,150,569 number of mapped paired reads (both in pair) = 16,269,724 number of mapped paired reads (singletons) = 276,311 number of mapped bases = 1,316,988,134 bp number of sequenced bases = 1,316,737,515 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 687,125 duplication rate = 3.82% >>>>>>> Insert size mean insert size = 39,123.5267 std insert size = 1,858,669.1067 median insert size = 214 >>>>>>> Mapping quality mean mapping quality = 52.7184 >>>>>>> ACTG content number of A's = 406,639,568 bp (30.88%) number of C's = 249,658,210 bp (18.96%) number of T's = 406,289,239 bp (30.86%) number of G's = 253,804,911 bp (19.28%) number of N's = 345,587 bp (0.03%) GC percentage = 38.24% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 4,627,128 number of insertions = 95,694 mapped reads with insertion percentage = 0.57% number of deletions = 123,517 mapped reads with deletion percentage = 0.74% homopolymer indels = 47.01% >>>>>>> Coverage mean coverageData = 0.4254X std coverageData = 1.7762X There is a 16.15% of reference with a coverageData >= 1X There is a 7.9% of reference with a coverageData >= 2X There is a 4.68% of reference with a coverageData >= 3X There is a 3.08% of reference with a coverageData >= 4X There is a 2.16% of reference with a coverageData >= 5X There is a 1.58% of reference with a coverageData >= 6X There is a 1.2% of reference with a coverageData >= 7X There is a 0.93% of reference with a coverageData >= 8X There is a 0.73% of reference with a coverageData >= 9X There is a 0.59% of reference with a coverageData >= 10X There is a 0.48% of reference with a coverageData >= 11X There is a 0.4% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.15% of reference with a coverageData >= 18X There is a 0.13% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.1% of reference with a coverageData >= 21X There is a 0.09% of reference with a coverageData >= 22X There is a 0.08% of reference with a coverageData >= 23X There is a 0.07% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% 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 89165193 0.35773308263893955 1.7523514723141471 chr2 243199373 123124595 0.5062701991423308 1.7435361201647166 chr3 198022430 94683369 0.47814466775304193 1.670454564282315 chr4 191154276 99106531 0.5184635838331966 1.7579730491548595 chr5 180915260 78687597 0.43494173459994473 1.6274913437710967 chr6 171115067 81519358 0.4764008186374377 1.928952360235517 chr7 159138663 135292045 0.8501519520746508 3.2765894785399285 chr8 146364022 93564462 0.6392586150714006 1.9377795278888985 chr9 141213431 49091357 0.34763943239931616 1.3873426608017643 chr10 135534747 22764670 0.16796187327519785 2.2879986877770997 chr11 135006516 52636932 0.3898843815805157 1.6477300245016508 chr12 133851895 57120320 0.4267427069299243 1.6438809048502632 chr13 115169878 49699673 0.4315336081193036 1.435329099439902 chr14 107349540 32837826 0.3058962898210835 1.2016961900073058 chr15 102531392 30902423 0.3013947474740224 1.2779905442865116 chr16 90354753 22538556 0.2494451620049252 1.1235310174609503 chr17 81195210 19207754 0.23656264944693167 1.1355439728556254 chr18 78077248 34367423 0.44017205883076205 1.6595280978940752 chr19 59128983 12501388 0.21142572332082898 1.1949259201486595 chr20 63025520 27835753 0.4416584424848855 1.6744685041372915 chr21 48129895 16774897 0.3485338374413657 1.359815354935545 chr22 51304566 6940168 0.13527388575901803 0.8431045275056295 chrMT 16571 936 0.05648421941946775 0.23525630613689333 chrX 155270560 85715593 0.5520402129032058 1.9204411661686298 chrY 59373566 909315 0.015315148832394538 0.21730312292969628