BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779392.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 = 6,789,370 number of mapped reads = 5,649,031 (83.2%) number of supplementary alignments = 19,311 (0.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,855,224 number of mapped paired reads (second in pair) = 2,793,807 number of mapped paired reads (both in pair) = 5,553,074 number of mapped paired reads (singletons) = 95,957 number of mapped bases = 448,526,869 bp number of sequenced bases = 448,431,942 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,747 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 42,686.9979 std insert size = 1,964,258.4432 median insert size = 352 >>>>>>> Mapping quality mean mapping quality = 53.4599 >>>>>>> ACTG content number of A's = 136,272,711 bp (30.39%) number of C's = 86,878,463 bp (19.37%) number of T's = 133,288,684 bp (29.72%) number of G's = 91,894,612 bp (20.49%) number of N's = 97,472 bp (0.02%) GC percentage = 39.87% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 2,155,314 number of insertions = 39,251 mapped reads with insertion percentage = 0.69% number of deletions = 46,244 mapped reads with deletion percentage = 0.81% homopolymer indels = 47.1% >>>>>>> Coverage mean coverageData = 0.1449X std coverageData = 0.5642X There is a 11.55% of reference with a coverageData >= 1X There is a 2.19% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% 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 37353672 0.14986390746043518 0.9667419909931073 chr2 243199373 39472824 0.16230643818312804 0.5382437111542105 chr3 198022430 31105128 0.15707881172855015 0.455150286059413 chr4 191154276 25224383 0.1319582461236703 0.41854118551898895 chr5 180915260 37357070 0.20648932544440973 0.5195801153302679 chr6 171115067 21186547 0.12381462001823604 0.41750582044442536 chr7 159138663 51931959 0.32633150248346626 0.9520064653287766 chr8 146364022 21351651 0.14588046097831336 0.43616645498902723 chr9 141213431 13017490 0.09218308703228094 0.39685012453050533 chr10 135534747 14225421 0.10495774194347372 0.7373082237959974 chr11 135006516 19877107 0.14723072329338532 0.46229312176268234 chr12 133851895 23878249 0.17839305898508198 0.4961657903395167 chr13 115169878 16809616 0.14595496923249324 0.44982264364877494 chr14 107349540 18735190 0.17452510742011562 0.5037812055115135 chr15 102531392 10725718 0.10460911327527866 0.37814653696008976 chr16 90354753 8150807 0.09020894562126687 0.363940540839513 chr17 81195210 10040368 0.12365714677011119 0.44389631362877446 chr18 78077248 9269657 0.11872417685623346 0.494697566478144 chr19 59128983 5507360 0.09314146329897134 0.7367446448628042 chr20 63025520 7892292 0.1252237506330769 0.41493804913120547 chr21 48129895 6077625 0.12627546766931447 0.4182535574886076 chr22 51304566 3899349 0.0760039369595291 0.3299383632167592 chrMT 16571 983 0.05932049966809486 0.28570934910536233 chrX 155270560 13468636 0.08674301168231763 0.3398503369084211 chrY 59373566 1967767 0.0331421393823642 0.20878755544191177