BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779414.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 = 14,158,556 number of mapped reads = 13,828,915 (97.67%) number of supplementary alignments = 56,744 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,958,228 number of mapped paired reads (second in pair) = 6,870,687 number of mapped paired reads (both in pair) = 13,716,288 number of mapped paired reads (singletons) = 112,627 number of mapped bases = 1,099,858,978 bp number of sequenced bases = 1,099,629,858 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 490,296 duplication rate = 3.24% >>>>>>> Insert size mean insert size = 83,387.4286 std insert size = 2,790,553.75 median insert size = 191 >>>>>>> Mapping quality mean mapping quality = 52.688 >>>>>>> ACTG content number of A's = 332,710,414 bp (30.26%) number of C's = 216,781,670 bp (19.71%) number of T's = 328,775,220 bp (29.9%) number of G's = 221,119,020 bp (20.11%) number of N's = 243,534 bp (0.02%) GC percentage = 39.82% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 3,669,601 number of insertions = 97,705 mapped reads with insertion percentage = 0.7% number of deletions = 111,133 mapped reads with deletion percentage = 0.79% homopolymer indels = 47.36% >>>>>>> Coverage mean coverageData = 0.3553X std coverageData = 1.3898X There is a 17.3% of reference with a coverageData >= 1X There is a 8% of reference with a coverageData >= 2X There is a 4.05% of reference with a coverageData >= 3X There is a 2.21% of reference with a coverageData >= 4X There is a 1.27% of reference with a coverageData >= 5X There is a 0.76% of reference with a coverageData >= 6X There is a 0.48% of reference with a coverageData >= 7X There is a 0.31% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% 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 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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% 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 81865162 0.328445167645139 2.434741777603766 chr2 243199373 89719467 0.3689132331767977 1.0192891207978099 chr3 198022430 31372835 0.15843071413677734 0.695207973507842 chr4 191154276 102134926 0.5343062584694679 1.1936732952943736 chr5 180915260 116854336 0.6459064647172383 1.3674410700213544 chr6 171115067 39931815 0.2333623549351151 1.0368816053001506 chr7 159138663 140824510 0.8849170110220167 2.4443602991467612 chr8 146364022 59618083 0.4073274441720384 1.147920453942347 chr9 141213431 43712979 0.30955255948706467 1.6513052455752992 chr10 135534747 16177818 0.11936288190363464 1.8392646115147824 chr11 135006516 57553086 0.4262985795441162 1.1557580614627916 chr12 133851895 69332276 0.51797754525627 1.181361008481482 chr13 115169878 41542826 0.3607091256969118 1.0068648918808158 chr14 107349540 35574163 0.33138626397467563 0.989846834176224 chr15 102531392 16254081 0.1585278487197365 0.6722854580338281 chr16 90354753 40839672 0.45199251443916844 1.1952667953304872 chr17 81195210 13684527 0.16853859975237456 0.9690481276453752 chr18 78077248 6991721 0.08954876329657521 0.843716988467289 chr19 59128983 17596320 0.2975921300726583 1.605887423054792 chr20 63025520 21875477 0.34708919498006524 0.9612946491995524 chr21 48129895 16549297 0.34384652200051546 1.0327234228432127 chr22 51304566 6820471 0.13294081856184106 0.5892781255327268 chrMT 16571 282 0.017017681491762717 0.12933707901606423 chrX 155270560 31989852 0.20602651268856118 0.7049727390653999 chrY 59373566 1042996 0.0175666726839348 0.22089418622008788