BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779410.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 = 15,407,908 number of mapped reads = 15,098,377 (97.99%) number of supplementary alignments = 54,303 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,604,938 number of mapped paired reads (second in pair) = 7,493,439 number of mapped paired reads (both in pair) = 14,960,882 number of mapped paired reads (singletons) = 137,495 number of mapped bases = 1,200,979,729 bp number of sequenced bases = 1,200,727,084 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 475,752 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 132,419.894 std insert size = 3,583,439.5231 median insert size = 186 >>>>>>> Mapping quality mean mapping quality = 52.9795 >>>>>>> ACTG content number of A's = 365,270,550 bp (30.42%) number of C's = 235,349,366 bp (19.6%) number of T's = 358,469,801 bp (29.85%) number of G's = 241,368,719 bp (20.1%) number of N's = 268,648 bp (0.02%) GC percentage = 39.7% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 3,969,762 number of insertions = 106,150 mapped reads with insertion percentage = 0.7% number of deletions = 122,307 mapped reads with deletion percentage = 0.8% homopolymer indels = 47.17% >>>>>>> Coverage mean coverageData = 0.388X std coverageData = 1.5047X There is a 20.61% of reference with a coverageData >= 1X There is a 9.04% of reference with a coverageData >= 2X There is a 4.26% of reference with a coverageData >= 3X There is a 2.15% of reference with a coverageData >= 4X There is a 1.12% of reference with a coverageData >= 5X There is a 0.61% of reference with a coverageData >= 6X There is a 0.34% of reference with a coverageData >= 7X There is a 0.19% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 113674137 0.4560636059558704 3.5775668868954886 chr2 243199373 115424556 0.47460877294284803 1.133576627158185 chr3 198022430 85977886 0.4341825620461278 1.0085974111934901 chr4 191154276 87664785 0.4586075019321043 1.034218101548396 chr5 180915260 105922776 0.5854828166512874 1.2400855844295509 chr6 171115067 63408969 0.37056332976218864 1.0299842622944724 chr7 159138663 104892559 0.659126808172317 1.712238100619583 chr8 146364022 90035538 0.6151480177280179 1.2959635547280481 chr9 141213431 48808647 0.3456374273634071 1.109787043063085 chr10 135534747 19500423 0.14387766555538706 1.9565674005909583 chr11 135006516 66744636 0.49438084899546625 1.1776413457812644 chr12 133851895 55212758 0.4124914182201156 1.0086191595189586 chr13 115169878 27769220 0.24111530273566845 0.7766298589075936 chr14 107349540 44330775 0.41295728887147537 1.021077451315102 chr15 102531392 24289048 0.23689377005629653 0.7679425231099266 chr16 90354753 10060879 0.11134864150422723 0.5145815267860037 chr17 81195210 16892656 0.20804990836282092 0.889296296010603 chr18 78077248 22100120 0.28305454618482456 1.0184775062635572 chr19 59128983 13438619 0.22727634263555657 1.9139163664689656 chr20 63025520 24920089 0.3953968011687964 1.0031847582780564 chr21 48129895 17289186 0.3592192752550156 0.9249911189250696 chr22 51304566 5917306 0.1153368298642269 0.5724184600711958 chrMT 16571 937 0.056544565807736404 0.3044554532875354 chrX 155270560 32576644 0.20980567082388316 0.7224582704627954 chrY 59373566 4126580 0.06950197331923773 0.41411992114629054