BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1778057.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 = 172,300,986 number of mapped reads = 162,733,539 (94.45%) number of supplementary alignments = 153,225 (0.09%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 82,177,317 number of mapped paired reads (second in pair) = 80,556,222 number of mapped paired reads (both in pair) = 160,450,044 number of mapped paired reads (singletons) = 2,283,495 number of mapped bases = 11,284,448,892 bp number of sequenced bases = 11,283,516,801 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,913,681 duplication rate = 51.6% >>>>>>> Insert size mean insert size = 19,395.8325 std insert size = 1,387,185.3272 median insert size = 103 >>>>>>> Mapping quality mean mapping quality = 52.0973 >>>>>>> ACTG content number of A's = 2,840,157,073 bp (25.17%) number of C's = 2,813,713,406 bp (24.94%) number of T's = 2,838,028,741 bp (25.15%) number of G's = 2,790,275,498 bp (24.73%) number of N's = 1,342,083 bp (0.01%) GC percentage = 49.67% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 56,565,640 number of insertions = 302,726 mapped reads with insertion percentage = 0.18% number of deletions = 443,360 mapped reads with deletion percentage = 0.27% homopolymer indels = 37.7% >>>>>>> Coverage mean coverageData = 3.6452X std coverageData = 36.6008X There is a 23.4% of reference with a coverageData >= 1X There is a 14.82% of reference with a coverageData >= 2X There is a 8.66% of reference with a coverageData >= 3X There is a 6.85% of reference with a coverageData >= 4X There is a 4.91% of reference with a coverageData >= 5X There is a 4.22% of reference with a coverageData >= 6X There is a 3.48% of reference with a coverageData >= 7X There is a 3.16% of reference with a coverageData >= 8X There is a 2.84% of reference with a coverageData >= 9X There is a 2.67% of reference with a coverageData >= 10X There is a 2.51% of reference with a coverageData >= 11X There is a 2.41% of reference with a coverageData >= 12X There is a 2.32% of reference with a coverageData >= 13X There is a 2.25% of reference with a coverageData >= 14X There is a 2.19% of reference with a coverageData >= 15X There is a 2.14% of reference with a coverageData >= 16X There is a 2.1% of reference with a coverageData >= 17X There is a 2.06% of reference with a coverageData >= 18X There is a 2.02% of reference with a coverageData >= 19X There is a 1.99% of reference with a coverageData >= 20X There is a 1.96% of reference with a coverageData >= 21X There is a 1.93% of reference with a coverageData >= 22X There is a 1.9% of reference with a coverageData >= 23X There is a 1.88% of reference with a coverageData >= 24X There is a 1.85% of reference with a coverageData >= 25X There is a 1.83% of reference with a coverageData >= 26X There is a 1.81% of reference with a coverageData >= 27X There is a 1.79% of reference with a coverageData >= 28X There is a 1.77% of reference with a coverageData >= 29X There is a 1.75% of reference with a coverageData >= 30X There is a 1.73% of reference with a coverageData >= 31X There is a 1.71% of reference with a coverageData >= 32X There is a 1.7% of reference with a coverageData >= 33X There is a 1.68% of reference with a coverageData >= 34X There is a 1.66% of reference with a coverageData >= 35X There is a 1.65% of reference with a coverageData >= 36X There is a 1.63% of reference with a coverageData >= 37X There is a 1.62% of reference with a coverageData >= 38X There is a 1.6% of reference with a coverageData >= 39X There is a 1.59% of reference with a coverageData >= 40X There is a 1.57% of reference with a coverageData >= 41X There is a 1.56% of reference with a coverageData >= 42X There is a 1.55% of reference with a coverageData >= 43X There is a 1.53% of reference with a coverageData >= 44X There is a 1.52% of reference with a coverageData >= 45X There is a 1.51% of reference with a coverageData >= 46X There is a 1.49% of reference with a coverageData >= 47X There is a 1.48% of reference with a coverageData >= 48X There is a 1.47% of reference with a coverageData >= 49X There is a 1.46% of reference with a coverageData >= 50X There is a 1.44% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1256038525 5.039259360561433 49.11972078578349 chr2 243199373 815912657 3.3549126666539557 34.18413078791667 chr3 198022430 614310682 3.1022277728841123 36.65089580265883 chr4 191154276 455875450 2.384856146247024 25.951493057668966 chr5 180915260 508923642 2.8130498333860836 27.09338410850207 chr6 171115067 574032707 3.354659043554592 38.24801028262042 chr7 159138663 561584992 3.5289035449543773 40.974779179759636 chr8 146364022 372669426 2.546181916208889 25.6943230229492 chr9 141213431 468560537 3.3181017816924228 31.302931005859932 chr10 135534747 475241448 3.5064177896757354 31.867367364799676 chr11 135006516 601730640 4.457048873107724 37.45035627964923 chr12 133851895 547946638 4.093678599021702 33.5039122332257 chr13 115169878 204733402 1.777664486194906 22.82576398332903 chr14 107349540 357724891 3.3323374371236243 32.60410248615764 chr15 102531392 413968290 4.037478492440637 36.540536123757285 chr16 90354753 470448751 5.2066851535745995 40.44174515389589 chr17 81195210 621978927 7.6602908841543735 56.70594778796295 chr18 78077248 176880969 2.265461111026864 25.11515645502555 chr19 59128983 611485691 10.341556035218803 58.81001047448437 chr20 63025520 249370370 3.9566570811315795 31.46335490002151 chr21 48129895 123879489 2.5738574538756005 28.79255404076187 chr22 51304566 222986382 4.346326250961757 34.380267864940876 chrMT 16571 523492 31.590851487538472 14.790804219216245 chrX 155270560 562494571 3.6226736800588597 46.50292796705872 chrY 59373566 15146323 0.25510212743495986 20.50652924743205