BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779294.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 = 13,007,720 number of mapped reads = 12,617,554 (97%) number of supplementary alignments = 30,326 (0.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,373,206 number of mapped paired reads (second in pair) = 6,244,348 number of mapped paired reads (both in pair) = 12,473,088 number of mapped paired reads (singletons) = 144,466 number of mapped bases = 1,004,204,274 bp number of sequenced bases = 1,004,012,589 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 168,867 duplication rate = 1.24% >>>>>>> Insert size mean insert size = 44,865.372 std insert size = 1,964,831.6324 median insert size = 198 >>>>>>> Mapping quality mean mapping quality = 52.8991 >>>>>>> ACTG content number of A's = 305,733,039 bp (30.45%) number of C's = 195,093,209 bp (19.43%) number of T's = 305,170,916 bp (30.4%) number of G's = 197,825,290 bp (19.7%) number of N's = 190,135 bp (0.02%) GC percentage = 39.13% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 3,924,991 number of insertions = 73,067 mapped reads with insertion percentage = 0.57% number of deletions = 92,665 mapped reads with deletion percentage = 0.73% homopolymer indels = 46.62% >>>>>>> Coverage mean coverageData = 0.3244X std coverageData = 0.9231X There is a 20.13% of reference with a coverageData >= 1X There is a 6.96% of reference with a coverageData >= 2X There is a 2.67% of reference with a coverageData >= 3X There is a 1.15% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.28% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.03% 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 0.02% 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 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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% 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 70243096 0.2818171353723528 0.9524231919494136 chr2 243199373 58509076 0.2405807024839657 0.6572010964249769 chr3 198022430 67019217 0.3384425542096418 0.8069137248749718 chr4 191154276 64639218 0.3381520903042734 0.800657198188369 chr5 180915260 64320594 0.355528848146917 0.8111398271703847 chr6 171115067 59858585 0.3498148120410694 0.836586150480118 chr7 159138663 85681002 0.5384046867353661 1.9574444542992897 chr8 146364022 76422947 0.5221429826518432 1.0250535447045188 chr9 141213431 39625720 0.2806087191522172 0.7853236021336344 chr10 135534747 20343664 0.1500992509323089 0.8453586733762226 chr11 135006516 49202505 0.3644454094349046 0.8542142476858373 chr12 133851895 55701246 0.416140884669582 0.9021121893242317 chr13 115169878 28757300 0.24969462935438727 0.6891775082152072 chr14 107349540 24756565 0.23061640506331 0.6710287988389683 chr15 102531392 27696631 0.2701283037296519 0.7452116997864582 chr16 90354753 19303654 0.21364292811469476 0.6188627465141179 chr17 81195210 18697600 0.23027959407950296 0.6702235260772283 chr18 78077248 26937154 0.34500644797316626 0.8264125836664816 chr19 59128983 11406910 0.19291571444751554 0.6883820692393923 chr20 63025520 24411512 0.3873274191153044 0.9162213565975906 chr21 48129895 10657293 0.2214277217932846 0.6408390849857946 chr22 51304566 6602659 0.12869534848028927 0.49400451550888425 chrMT 16571 455 0.027457606662241264 0.20294536132442598 chrX 155270560 92520081 0.5958636395721121 1.1810010280228191 chrY 59373566 889590 0.014982930282476211 0.17175646202228576