BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779376.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 = 21,912,028 number of mapped reads = 18,327,900 (83.64%) number of supplementary alignments = 222,151 (1.01%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,224,093 number of mapped paired reads (second in pair) = 9,103,807 number of mapped paired reads (both in pair) = 18,005,268 number of mapped paired reads (singletons) = 322,632 number of mapped bases = 1,451,126,669 bp number of sequenced bases = 1,450,783,469 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,884,823 duplication rate = 16.93% >>>>>>> Insert size mean insert size = 289,455.9778 std insert size = 5,193,049.2418 median insert size = 162 >>>>>>> Mapping quality mean mapping quality = 52.3256 >>>>>>> ACTG content number of A's = 455,770,879 bp (31.42%) number of C's = 271,074,441 bp (18.68%) number of T's = 446,175,881 bp (30.75%) number of G's = 277,448,450 bp (19.12%) number of N's = 313,818 bp (0.02%) GC percentage = 37.81% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 4,846,303 number of insertions = 172,280 mapped reads with insertion percentage = 0.93% number of deletions = 162,002 mapped reads with deletion percentage = 0.84% homopolymer indels = 46.27% >>>>>>> Coverage mean coverageData = 0.4688X std coverageData = 44.8753X There is a 6.02% of reference with a coverageData >= 1X There is a 3.3% of reference with a coverageData >= 2X There is a 2.17% of reference with a coverageData >= 3X There is a 1.64% of reference with a coverageData >= 4X There is a 1.31% of reference with a coverageData >= 5X There is a 1.08% of reference with a coverageData >= 6X There is a 0.92% of reference with a coverageData >= 7X There is a 0.79% of reference with a coverageData >= 8X There is a 0.69% of reference with a coverageData >= 9X There is a 0.61% of reference with a coverageData >= 10X There is a 0.55% of reference with a coverageData >= 11X There is a 0.5% of reference with a coverageData >= 12X There is a 0.45% of reference with a coverageData >= 13X There is a 0.41% of reference with a coverageData >= 14X There is a 0.38% of reference with a coverageData >= 15X There is a 0.35% of reference with a coverageData >= 16X There is a 0.32% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.17% of reference with a coverageData >= 28X There is a 0.16% of reference with a coverageData >= 29X There is a 0.15% of reference with a coverageData >= 30X There is a 0.15% of reference with a coverageData >= 31X There is a 0.14% of reference with a coverageData >= 32X There is a 0.13% of reference with a coverageData >= 33X There is a 0.13% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.11% of reference with a coverageData >= 38X There is a 0.11% of reference with a coverageData >= 39X There is a 0.1% of reference with a coverageData >= 40X There is a 0.1% of reference with a coverageData >= 41X There is a 0.1% of reference with a coverageData >= 42X There is a 0.09% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.09% of reference with a coverageData >= 45X There is a 0.09% of reference with a coverageData >= 46X There is a 0.08% of reference with a coverageData >= 47X There is a 0.08% of reference with a coverageData >= 48X There is a 0.08% of reference with a coverageData >= 49X There is a 0.08% of reference with a coverageData >= 50X There is a 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 152701851 0.6126438136336679 77.0044057830392 chr2 243199373 244922037 1.0070833406301587 125.26562348292796 chr3 198022430 100592741 0.5079866003058341 15.836254746667644 chr4 191154276 105401908 0.5513970715465449 29.82738106426455 chr5 180915260 154266842 0.852702209863336 35.069975884311134 chr6 171115067 79359508 0.4637786104481378 8.213533445804762 chr7 159138663 134196594 0.8432683263148943 20.64636991408752 chr8 146364022 57348222 0.3918191179523613 32.39129853525668 chr9 141213431 30027343 0.21263801033203422 9.706377405040568 chr10 135534747 26392269 0.19472695809879662 5.5579604275067025 chr11 135006516 80741688 0.5980577115255682 23.08726636574356 chr12 133851895 41106482 0.30710422142323796 5.072440410979833 chr13 115169878 39292133 0.3411667502157118 18.333158745928124 chr14 107349540 26106364 0.2431902735680097 3.483596783114251 chr15 102531392 13905101 0.1356179871233973 2.6101324999507245 chr16 90354753 26862479 0.29730012100193554 20.801870815062156 chr17 81195210 11828239 0.14567656146218477 3.937565473588318 chr18 78077248 32897379 0.42134398743152424 20.000917188224893 chr19 59128983 11055984 0.18698079079087154 9.891317733103078 chr20 63025520 11795894 0.18716059780228708 2.88197994460688 chr21 48129895 25757937 0.535175424754199 27.755514983131146 chr22 51304566 4519171 0.08808516185479476 1.802677388201525 chrMT 16571 196103 11.834107778649448 6.94229512757972 chrX 155270560 34579473 0.22270463248152128 9.862441210030406 chrY 59373566 5272927 0.08880933646464825 3.4079665224490276