BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1264616.sorted.bam outfile = /home/yangyx/scDNA/SRP041470/SRP041470.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 = 1,195,630,648 number of mapped reads = 1,189,184,192 (99.46%) number of supplementary alignments = 11,192,320 (0.94%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 595,902,050 number of mapped paired reads (second in pair) = 593,282,142 number of mapped paired reads (both in pair) = 1,185,322,156 number of mapped paired reads (singletons) = 3,862,036 number of mapped bases = 118,053,658,151 bp number of sequenced bases = 118,026,504,729 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 445,683,344 duplication rate = 37.12% >>>>>>> Insert size mean insert size = 113,324.7511 std insert size = 3,222,760.1459 median insert size = 302 >>>>>>> Mapping quality mean mapping quality = 54.3382 >>>>>>> ACTG content number of A's = 36,395,159,251 bp (30.84%) number of C's = 22,472,617,939 bp (19.04%) number of T's = 36,304,127,852 bp (30.76%) number of G's = 22,788,546,333 bp (19.31%) number of N's = 66,053,354 bp (0.06%) GC percentage = 38.35% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 458,633,750 number of insertions = 12,527,101 mapped reads with insertion percentage = 1.04% number of deletions = 12,032,916 mapped reads with deletion percentage = 0.99% homopolymer indels = 47.05% >>>>>>> Coverage mean coverageData = 38.1348X std coverageData = 38.3681X There is a 90.19% of reference with a coverageData >= 1X There is a 88.56% of reference with a coverageData >= 2X There is a 86.95% of reference with a coverageData >= 3X There is a 85.36% of reference with a coverageData >= 4X There is a 83.77% of reference with a coverageData >= 5X There is a 82.2% of reference with a coverageData >= 6X There is a 80.63% of reference with a coverageData >= 7X There is a 79.08% of reference with a coverageData >= 8X There is a 77.54% of reference with a coverageData >= 9X There is a 76.02% of reference with a coverageData >= 10X There is a 74.5% of reference with a coverageData >= 11X There is a 73% of reference with a coverageData >= 12X There is a 71.51% of reference with a coverageData >= 13X There is a 70.03% of reference with a coverageData >= 14X There is a 68.57% of reference with a coverageData >= 15X There is a 67.12% of reference with a coverageData >= 16X There is a 65.69% of reference with a coverageData >= 17X There is a 64.27% of reference with a coverageData >= 18X There is a 62.87% of reference with a coverageData >= 19X There is a 61.48% of reference with a coverageData >= 20X There is a 60.11% of reference with a coverageData >= 21X There is a 58.75% of reference with a coverageData >= 22X There is a 57.41% of reference with a coverageData >= 23X There is a 56.09% of reference with a coverageData >= 24X There is a 54.79% of reference with a coverageData >= 25X There is a 53.51% of reference with a coverageData >= 26X There is a 52.25% of reference with a coverageData >= 27X There is a 51% of reference with a coverageData >= 28X There is a 49.78% of reference with a coverageData >= 29X There is a 48.57% of reference with a coverageData >= 30X There is a 47.39% of reference with a coverageData >= 31X There is a 46.22% of reference with a coverageData >= 32X There is a 45.08% of reference with a coverageData >= 33X There is a 43.95% of reference with a coverageData >= 34X There is a 42.85% of reference with a coverageData >= 35X There is a 41.76% of reference with a coverageData >= 36X There is a 40.7% of reference with a coverageData >= 37X There is a 39.66% of reference with a coverageData >= 38X There is a 38.64% of reference with a coverageData >= 39X There is a 37.64% of reference with a coverageData >= 40X There is a 36.66% of reference with a coverageData >= 41X There is a 35.7% of reference with a coverageData >= 42X There is a 34.77% of reference with a coverageData >= 43X There is a 33.85% of reference with a coverageData >= 44X There is a 32.95% of reference with a coverageData >= 45X There is a 32.07% of reference with a coverageData >= 46X There is a 31.21% of reference with a coverageData >= 47X There is a 30.37% of reference with a coverageData >= 48X There is a 29.55% of reference with a coverageData >= 49X There is a 28.74% of reference with a coverageData >= 50X There is a 27.96% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9293893492 37.287343376368156 39.740366969846754 chr2 243199373 10695836520 43.97970433912262 39.00339498211585 chr3 198022430 8950839247 45.201138310442914 37.760973387254786 chr4 191154276 9841867976 51.48651749752122 40.531954774933766 chr5 180915260 8216366410 45.415552065646644 37.818155051499815 chr6 171115067 7990651946 46.697535676387865 39.999339170953064 chr7 159138663 6687752752 42.024688569866896 39.765987724182594 chr8 146364022 6815165736 46.56312147530354 38.67231553528726 chr9 141213431 5189468414 36.74911357404807 41.157761277976284 chr10 135534747 5045016271 37.22304709802572 35.32422517054637 chr11 135006516 5138883113 38.06396361639315 37.57677866450023 chr12 133851895 5732994840 42.83088289485928 40.06491312488019 chr13 115169878 4735833654 41.12041912556337 39.23409721646066 chr14 107349540 3871175847 36.061410668364296 39.379062033849024 chr15 102531392 3174908483 30.965233389204354 37.72148280806466 chr16 90354753 2200603330 24.355147426500075 30.128692713501263 chr17 81195210 1865041562 22.969847137534344 28.422655858376956 chr18 78077248 3399500389 43.540217874994774 38.00220891258641 chr19 59128983 868517355 14.6885217863463 21.411158254225068 chr20 63025520 1857820689 29.477276649204956 37.73083117237372 chr21 48129895 1497025508 31.10385983597097 40.17568477620926 chr22 51304566 605122358 11.794707667929595 20.004426910206096 chrMT 16571 409806 24.73031199082735 6.803717751704135 chrX 155270560 3826347557 24.643097551783157 25.7142992677034 chrY 59373566 552614896 9.307423037383337 20.232947111769807