BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779079.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 = 37,078,208 number of mapped reads = 35,926,236 (96.89%) number of supplementary alignments = 206,780 (0.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 18,094,736 number of mapped paired reads (second in pair) = 17,831,500 number of mapped paired reads (both in pair) = 35,529,380 number of mapped paired reads (singletons) = 396,856 number of mapped bases = 3,586,790,264 bp number of sequenced bases = 3,585,962,671 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,829,515 duplication rate = 4.4% >>>>>>> Insert size mean insert size = 75,140.8285 std insert size = 2,642,912.3153 median insert size = 214 >>>>>>> Mapping quality mean mapping quality = 53.6755 >>>>>>> ACTG content number of A's = 1,093,311,619 bp (30.49%) number of C's = 697,586,297 bp (19.45%) number of T's = 1,082,030,619 bp (30.17%) number of G's = 711,828,553 bp (19.85%) number of N's = 1,205,583 bp (0.03%) GC percentage = 39.3% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 16,549,645 number of insertions = 300,717 mapped reads with insertion percentage = 0.83% number of deletions = 369,978 mapped reads with deletion percentage = 1.01% homopolymer indels = 46.87% >>>>>>> Coverage mean coverageData = 1.1586X std coverageData = 3.5152X There is a 34.79% of reference with a coverageData >= 1X There is a 21.6% of reference with a coverageData >= 2X There is a 14.27% of reference with a coverageData >= 3X There is a 9.97% of reference with a coverageData >= 4X There is a 7.2% of reference with a coverageData >= 5X There is a 5.33% of reference with a coverageData >= 6X There is a 4.03% of reference with a coverageData >= 7X There is a 3.09% of reference with a coverageData >= 8X There is a 2.41% of reference with a coverageData >= 9X There is a 1.9% of reference with a coverageData >= 10X There is a 1.52% of reference with a coverageData >= 11X There is a 1.22% of reference with a coverageData >= 12X There is a 1% of reference with a coverageData >= 13X There is a 0.82% of reference with a coverageData >= 14X There is a 0.68% of reference with a coverageData >= 15X There is a 0.56% of reference with a coverageData >= 16X There is a 0.48% of reference with a coverageData >= 17X There is a 0.4% of reference with a coverageData >= 18X There is a 0.34% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.19% of reference with a coverageData >= 23X There is a 0.17% of reference with a coverageData >= 24X There is a 0.15% of reference with a coverageData >= 25X There is a 0.13% of reference with a coverageData >= 26X There is a 0.12% of reference with a coverageData >= 27X There is a 0.11% of reference with a coverageData >= 28X There is a 0.1% of reference with a coverageData >= 29X There is a 0.09% of reference with a coverageData >= 30X There is a 0.08% of reference with a coverageData >= 31X There is a 0.07% of reference with a coverageData >= 32X There is a 0.07% of reference with a coverageData >= 33X There is a 0.06% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 261242007 1.0481097537566415 3.790617068437238 chr2 243199373 254260002 1.0454796772851878 2.761969394664497 chr3 198022430 264464547 1.3355282378869908 2.7790634104254344 chr4 191154276 230187099 1.2041953955557865 2.647314475817185 chr5 180915260 215036234 1.1886019675731059 2.6527062770916596 chr6 171115067 243401291 1.4224421920718413 2.9975544735758524 chr7 159138663 289447094 1.818835778455673 8.885660602489546 chr8 146364022 292389559 1.9976873756584799 3.6645577825007134 chr9 141213431 185328227 1.3123980182876513 3.1218465183552766 chr10 135534747 79020790 0.5830297525106237 4.323305278097652 chr11 135006516 139612037 1.03411332383394 2.504729397087979 chr12 133851895 164304154 1.2275071189690665 2.7609817886943464 chr13 115169878 102321970 0.888443851611964 2.3630340349181767 chr14 107349540 123490946 1.1503630662972566 2.705573837773334 chr15 102531392 101451118 0.9894639682644707 2.6081011658140323 chr16 90354753 99296900 1.0989670903090178 2.6087638146133467 chr17 81195210 76346210 0.9402797283238753 2.443481344566208 chr18 78077248 66781403 0.8553247547864392 2.2827085262006808 chr19 59128983 50799549 0.8591311134169177 2.5691415635352977 chr20 63025520 66027101 1.0476248510127326 2.4525673450831307 chr21 48129895 38091586 0.7914329752849035 2.1858339375388995 chr22 51304566 25678458 0.5005101885083678 1.4643442846762407 chrMT 16571 23889 1.4416148693500694 1.3858520461306916 chrX 155270560 215824851 1.3899920950887277 3.293404942563672 chrY 59373566 1963242 0.03306592701539941 0.47634694456879256