BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779283.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 = 7,602,682 number of mapped reads = 7,367,259 (96.9%) number of supplementary alignments = 17,950 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,707,049 number of mapped paired reads (second in pair) = 3,660,210 number of mapped paired reads (both in pair) = 7,308,578 number of mapped paired reads (singletons) = 58,681 number of mapped bases = 586,078,686 bp number of sequenced bases = 585,966,925 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 69,634 duplication rate = 0.83% >>>>>>> Insert size mean insert size = 53,681.3807 std insert size = 2,202,186.7079 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 53.2215 >>>>>>> ACTG content number of A's = 178,656,580 bp (30.49%) number of C's = 113,562,986 bp (19.38%) number of T's = 177,733,360 bp (30.33%) number of G's = 115,902,559 bp (19.78%) number of N's = 111,440 bp (0.02%) GC percentage = 39.16% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 2,367,236 number of insertions = 42,731 mapped reads with insertion percentage = 0.58% number of deletions = 53,863 mapped reads with deletion percentage = 0.72% homopolymer indels = 46.7% >>>>>>> Coverage mean coverageData = 0.1893X std coverageData = 0.65X There is a 14.18% of reference with a coverageData >= 1X There is a 3.24% of reference with a coverageData >= 2X There is a 0.82% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% 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 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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% 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 47709379 0.1914112743574669 0.7796812569607632 chr2 243199373 47331511 0.19462020159073354 0.5282168169828507 chr3 198022430 38455933 0.19419988432623517 0.5176055549169272 chr4 191154276 42376224 0.22168598519867797 0.5634150765767586 chr5 180915260 37908290 0.2095361662692246 0.5400030259603487 chr6 171115067 31966880 0.1868151096244494 0.5169863694355733 chr7 159138663 59291886 0.3725800184710613 1.5228313273455643 chr8 146364022 44446483 0.3036708228747636 0.670121557883874 chr9 141213431 21121201 0.14956934939141872 0.4803358137735504 chr10 135534747 11566289 0.0853381826875731 0.8166568371409229 chr11 135006516 28392652 0.21030578998127764 0.5506642548739208 chr12 133851895 19693890 0.14713194759028253 0.4486384982604311 chr13 115169878 23990532 0.20830561268806763 0.5521293111068948 chr14 107349540 16468302 0.1534082214045817 0.47055334758873035 chr15 102531392 16470464 0.1606382560377216 0.48838670869659073 chr16 90354753 11049737 0.12229281397072714 0.41113281161875004 chr17 81195210 9416628 0.11597516651536464 0.40627803958924724 chr18 78077248 14861569 0.1903444265863469 0.5313081151227287 chr19 59128983 7420083 0.12548977884500398 0.5621364318341455 chr20 63025520 13747967 0.2181333370990037 0.5731733065220966 chr21 48129895 6901099 0.14338487545007111 0.4576629404980001 chr22 51304566 3412033 0.06650544514887817 0.3041439888619975 chrMT 16571 877 0.05292378251161668 0.22856370417006094 chrX 155270560 31652615 0.20385458131921466 0.5568906504994658 chrY 59373566 426162 0.007177638614463548 0.10684678943501609