BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779027.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 = 25,149,442 number of mapped reads = 24,428,661 (97.13%) number of supplementary alignments = 135,441 (0.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,293,327 number of mapped paired reads (second in pair) = 12,135,334 number of mapped paired reads (both in pair) = 24,170,316 number of mapped paired reads (singletons) = 258,345 number of mapped bases = 2,435,852,087 bp number of sequenced bases = 2,435,288,148 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,102,833 duplication rate = 4.06% >>>>>>> Insert size mean insert size = 54,074.2282 std insert size = 2,151,015.3522 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 53.2114 >>>>>>> ACTG content number of A's = 751,294,501 bp (30.85%) number of C's = 464,063,789 bp (19.06%) number of T's = 747,719,492 bp (30.7%) number of G's = 471,386,331 bp (19.36%) number of N's = 824,035 bp (0.03%) GC percentage = 38.41% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 11,138,420 number of insertions = 206,974 mapped reads with insertion percentage = 0.83% number of deletions = 254,713 mapped reads with deletion percentage = 1.02% homopolymer indels = 46.71% >>>>>>> Coverage mean coverageData = 0.7869X std coverageData = 2.6293X There is a 26.3% of reference with a coverageData >= 1X There is a 15.59% of reference with a coverageData >= 2X There is a 9.83% of reference with a coverageData >= 3X There is a 6.66% of reference with a coverageData >= 4X There is a 4.68% of reference with a coverageData >= 5X There is a 3.39% of reference with a coverageData >= 6X There is a 2.5% of reference with a coverageData >= 7X There is a 1.88% of reference with a coverageData >= 8X There is a 1.44% of reference with a coverageData >= 9X There is a 1.11% of reference with a coverageData >= 10X There is a 0.87% of reference with a coverageData >= 11X There is a 0.69% of reference with a coverageData >= 12X There is a 0.55% of reference with a coverageData >= 13X There is a 0.44% of reference with a coverageData >= 14X There is a 0.36% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.2% of reference with a coverageData >= 18X There is a 0.17% of reference with a coverageData >= 19X There is a 0.14% of reference with a coverageData >= 20X There is a 0.12% of reference with a coverageData >= 21X There is a 0.1% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 82666273 0.33165924589612156 3.4184337795398125 chr2 243199373 175330211 0.7209320025672928 2.1069332399448015 chr3 198022430 179909670 0.9085317759205359 2.1618139535329792 chr4 191154276 257146300 1.3452291279113213 2.704749466228725 chr5 180915260 197900007 1.0938823347461126 2.4240990343543696 chr6 171115067 115029818 0.672236641791456 1.9152373722512719 chr7 159138663 224775646 1.4124515172029566 5.031169652702554 chr8 146364022 203618804 1.39118070969654 2.7931245084408958 chr9 141213431 74366530 0.5266250488595522 1.9637738386679968 chr10 135534747 32207545 0.23763312149024043 3.7092861249041302 chr11 135006516 101683345 0.7531736097833974 1.966259785399049 chr12 133851895 105119941 0.7853451831966967 2.073195754055101 chr13 115169878 103734663 0.9007100189860408 2.226771825860317 chr14 107349540 91961638 0.8566560974550985 2.1651287485961337 chr15 102531392 37175159 0.36257343507050016 1.2732112978716574 chr16 90354753 37995332 0.4205128201722825 1.3884065205476401 chr17 81195210 35663188 0.43922773276896504 1.691819117171207 chr18 78077248 116531193 1.4925115316564437 3.040719237016246 chr19 59128983 18717202 0.31654868814503373 2.036711842846011 chr20 63025520 43364213 0.6880421296008347 1.7851083783143982 chr21 48129895 13525718 0.2810252962322066 1.0872028668427987 chr22 51304566 7488457 0.14596082929538864 0.7908393457570196 chrMT 16571 2132 0.12865849978878763 0.6322312683736306 chrX 155270560 178397695 1.148947327812819 2.9122832185843825 chrY 59373566 1541407 0.02596116595051744 0.4732211064170757