BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779202.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 = 9,587,008 number of mapped reads = 8,871,184 (92.53%) number of supplementary alignments = 27,536 (0.29%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,513,464 number of mapped paired reads (second in pair) = 4,357,720 number of mapped paired reads (both in pair) = 8,691,132 number of mapped paired reads (singletons) = 180,052 number of mapped bases = 704,912,952 bp number of sequenced bases = 704,765,952 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 120,567 duplication rate = 1.05% >>>>>>> Insert size mean insert size = 41,973.5687 std insert size = 1,991,479.1433 median insert size = 292 >>>>>>> Mapping quality mean mapping quality = 53.3703 >>>>>>> ACTG content number of A's = 213,246,214 bp (30.26%) number of C's = 137,572,323 bp (19.52%) number of T's = 212,000,056 bp (30.08%) number of G's = 141,819,108 bp (20.12%) number of N's = 128,251 bp (0.02%) GC percentage = 39.64% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 3,660,804 number of insertions = 60,566 mapped reads with insertion percentage = 0.68% number of deletions = 71,792 mapped reads with deletion percentage = 0.8% homopolymer indels = 47.56% >>>>>>> Coverage mean coverageData = 0.2277X std coverageData = 0.9035X There is a 17.6% of reference with a coverageData >= 1X There is a 3.6% of reference with a coverageData >= 2X There is a 0.78% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% 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 0.02% 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 52861265 0.21208077551790733 1.8549277512964297 chr2 243199373 54020009 0.22212232019200148 0.5729882583602237 chr3 198022430 44725140 0.2258589595128188 0.5331019183115453 chr4 191154276 41538275 0.21730235843638673 0.5303321788468037 chr5 180915260 45261293 0.25017952051142617 0.5629295270393692 chr6 171115067 39622072 0.23155221041990418 0.5899108476167045 chr7 159138663 68750522 0.4320164610155107 1.771640662640211 chr8 146364022 51159501 0.34953604240255165 0.696067707158309 chr9 141213431 27238245 0.19288707035239444 0.5988774277345028 chr10 135534747 18319194 0.1351623432771819 1.3811390958465182 chr11 135006516 33046868 0.2447798001097962 0.5759739019157223 chr12 133851895 30439094 0.22740876399247092 0.5427801949681326 chr13 115169878 21424601 0.1860260805347037 0.48848152514453425 chr14 107349540 23529116 0.21918227129804188 0.540393170874072 chr15 102531392 16924229 0.1650638762419221 0.46955155295518103 chr16 90354753 17313226 0.19161389329457854 0.5056804809831256 chr17 81195210 16135288 0.19872216599969383 0.6677666861163869 chr18 78077248 19737409 0.252793348966398 0.7355769998869711 chr19 59128983 11816430 0.19984159037540017 1.3252438474882202 chr20 63025520 17605398 0.2793376080038689 0.613813732542606 chr21 48129895 10209491 0.21212369152270122 0.5493278306318067 chr22 51304566 6119884 0.11928536731019224 0.40034209687725475 chrMT 16571 2080 0.1255204875988172 0.40565948200395563 chrX 155270560 36577273 0.23557120551378188 0.5653181265359485 chrY 59373566 537049 0.00904525424664572 0.12963687577415914