BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779416.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 = 16,797,054 number of mapped reads = 16,148,023 (96.14%) number of supplementary alignments = 108,544 (0.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,132,470 number of mapped paired reads (second in pair) = 8,015,553 number of mapped paired reads (both in pair) = 15,970,686 number of mapped paired reads (singletons) = 177,337 number of mapped bases = 1,281,017,665 bp number of sequenced bases = 1,280,734,291 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,047,156 duplication rate = 9.89% >>>>>>> Insert size mean insert size = 60,364.5335 std insert size = 2,291,817.7435 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 52.1831 >>>>>>> ACTG content number of A's = 400,723,387 bp (31.29%) number of C's = 239,364,654 bp (18.69%) number of T's = 395,673,870 bp (30.89%) number of G's = 244,686,847 bp (19.11%) number of N's = 285,533 bp (0.02%) GC percentage = 37.79% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 5,675,764 number of insertions = 124,481 mapped reads with insertion percentage = 0.76% number of deletions = 142,593 mapped reads with deletion percentage = 0.87% homopolymer indels = 45.05% >>>>>>> Coverage mean coverageData = 0.4138X std coverageData = 9.924X There is a 9.91% of reference with a coverageData >= 1X There is a 5.44% of reference with a coverageData >= 2X There is a 3.57% of reference with a coverageData >= 3X There is a 2.6% of reference with a coverageData >= 4X There is a 1.99% of reference with a coverageData >= 5X There is a 1.59% of reference with a coverageData >= 6X There is a 1.3% of reference with a coverageData >= 7X There is a 1.08% of reference with a coverageData >= 8X There is a 0.91% of reference with a coverageData >= 9X There is a 0.78% of reference with a coverageData >= 10X There is a 0.68% of reference with a coverageData >= 11X There is a 0.59% of reference with a coverageData >= 12X There is a 0.52% of reference with a coverageData >= 13X There is a 0.46% of reference with a coverageData >= 14X There is a 0.4% of reference with a coverageData >= 15X There is a 0.36% of reference with a coverageData >= 16X There is a 0.32% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.18% of reference with a coverageData >= 23X There is a 0.17% of reference with a coverageData >= 24X There is a 0.16% of reference with a coverageData >= 25X There is a 0.15% of reference with a coverageData >= 26X There is a 0.13% of reference with a coverageData >= 27X There is a 0.13% of reference with a coverageData >= 28X There is a 0.12% of reference with a coverageData >= 29X There is a 0.11% of reference with a coverageData >= 30X There is a 0.1% of reference with a coverageData >= 31X There is a 0.1% of reference with a coverageData >= 32X There is a 0.09% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.08% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.07% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.06% of reference with a coverageData >= 41X There is a 0.06% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.05% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 94142391 0.3777017309818458 19.415594255967058 chr2 243199373 99506125 0.4091545293580999 4.4693507016417415 chr3 198022430 122189120 0.6170468668625064 19.89426446945142 chr4 191154276 97937258 0.5123466764614777 3.3780729095680204 chr5 180915260 97087124 0.5366441946356543 5.557189573019517 chr6 171115067 75585361 0.44172241711479443 4.484325597999898 chr7 159138663 77264409 0.48551626326029895 12.923533284890901 chr8 146364022 77165084 0.527213470534446 14.819875182961567 chr9 141213431 63751413 0.45145431669314795 6.46503694772239 chr10 135534747 58566498 0.432114268085069 12.821210139821146 chr11 135006516 56204741 0.41631132085506156 6.0327825724690705 chr12 133851895 55533720 0.4148893073198553 6.226998642852161 chr13 115169878 49636830 0.4309879532910506 2.423863619972562 chr14 107349540 40104463 0.37358765580178543 3.984665986850577 chr15 102531392 21307626 0.20781563172379441 2.6697382319444247 chr16 90354753 23139613 0.256097352178031 3.132230287169659 chr17 81195210 15771040 0.19423608855744076 3.5029742074783905 chr18 78077248 35932417 0.46021623354347735 6.859410708460837 chr19 59128983 13461102 0.2276565791770848 11.469662545360782 chr20 63025520 16494813 0.2617164126531602 4.166644066785224 chr21 48129895 24135103 0.501457628361749 2.9918470975701124 chr22 51304566 4098823 0.07989197296786411 0.7274747442186623 chrMT 16571 534505 32.255446261541245 12.86187453830449 chrX 155270560 50363636 0.32436049692871594 2.713503984064928 chrY 59373566 11104450 0.18702683278279092 2.1312741755589375