BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779288.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 = 12,724,452 number of mapped reads = 12,329,113 (96.89%) number of supplementary alignments = 31,028 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,232,178 number of mapped paired reads (second in pair) = 6,096,935 number of mapped paired reads (both in pair) = 12,174,772 number of mapped paired reads (singletons) = 154,341 number of mapped bases = 981,275,264 bp number of sequenced bases = 981,087,917 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 315,516 duplication rate = 2.26% >>>>>>> Insert size mean insert size = 41,883.103 std insert size = 1,927,562.769 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 52.5908 >>>>>>> ACTG content number of A's = 302,876,402 bp (30.87%) number of C's = 186,478,191 bp (19.01%) number of T's = 302,045,571 bp (30.79%) number of G's = 189,502,197 bp (19.32%) number of N's = 185,556 bp (0.02%) GC percentage = 38.32% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 3,620,544 number of insertions = 71,214 mapped reads with insertion percentage = 0.57% number of deletions = 91,043 mapped reads with deletion percentage = 0.73% homopolymer indels = 46.73% >>>>>>> Coverage mean coverageData = 0.317X std coverageData = 1.3429X There is a 15.07% of reference with a coverageData >= 1X There is a 6.66% of reference with a coverageData >= 2X There is a 3.46% of reference with a coverageData >= 3X There is a 2.01% of reference with a coverageData >= 4X There is a 1.25% of reference with a coverageData >= 5X There is a 0.82% of reference with a coverageData >= 6X There is a 0.56% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.21% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% 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 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 68318175 0.27409430205592145 1.7785985620567561 chr2 243199373 88236134 0.3628139863666507 1.1504737625816794 chr3 198022430 82915795 0.4187192077180348 1.264550902800433 chr4 191154276 58282895 0.30489977111471994 1.0732443239550808 chr5 180915260 84070268 0.46469417781562483 1.3539075406513073 chr6 171115067 56839181 0.33216935245100304 1.074887200152865 chr7 159138663 72425078 0.45510673920893757 1.9160694335639101 chr8 146364022 84340422 0.576237389814281 1.6410666242328946 chr9 141213431 37700438 0.26697487436588097 1.0765414636996171 chr10 135534747 19715941 0.14546779653486203 2.71230247758164 chr11 135006516 39844802 0.29513243642255016 1.0444441378614167 chr12 133851895 58353524 0.43595590484542635 1.3103456499954216 chr13 115169878 36127971 0.31369288243927806 1.0488874249766047 chr14 107349540 30090834 0.2803070604680747 1.0118817971625385 chr15 102531392 24809615 0.24197091755079264 1.0008255402293869 chr16 90354753 14107585 0.15613550512389757 0.6908561912544466 chr17 81195210 11126125 0.13702932722262803 0.601938059054949 chr18 78077248 26168754 0.3351649125747875 1.0493575364926189 chr19 59128983 7092335 0.11994684569494456 0.9451602107807807 chr20 63025520 13996316 0.22207378852249057 0.7810277286717733 chr21 48129895 7871842 0.1635541070679668 0.7142701221771908 chr22 51304566 3374357 0.06577108555990903 0.37429496563044146 chrMT 16571 240 0.014483133184478908 0.134668262359154 chrX 155270560 54621745 0.35178429832416397 1.1935125409992922 chrY 59373566 844892 0.014230103679472444 0.21753305899133948