BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779157.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 = 38,312,532 number of mapped reads = 37,303,688 (97.37%) number of supplementary alignments = 225,172 (0.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 18,777,887 number of mapped paired reads (second in pair) = 18,525,801 number of mapped paired reads (both in pair) = 36,915,384 number of mapped paired reads (singletons) = 388,304 number of mapped bases = 3,726,196,839 bp number of sequenced bases = 3,725,344,670 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,865,500 duplication rate = 6.55% >>>>>>> Insert size mean insert size = 68,165.0561 std insert size = 2,502,078.9075 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 53.4743 >>>>>>> ACTG content number of A's = 1,147,927,499 bp (30.81%) number of C's = 712,838,192 bp (19.13%) number of T's = 1,137,564,501 bp (30.54%) number of G's = 725,502,809 bp (19.47%) number of N's = 1,511,669 bp (0.04%) GC percentage = 38.61% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 15,334,237 number of insertions = 305,554 mapped reads with insertion percentage = 0.81% number of deletions = 380,140 mapped reads with deletion percentage = 1% homopolymer indels = 46.34% >>>>>>> Coverage mean coverageData = 1.2037X std coverageData = 4.837X There is a 28.07% of reference with a coverageData >= 1X There is a 18.03% of reference with a coverageData >= 2X There is a 12.62% of reference with a coverageData >= 3X There is a 9.46% of reference with a coverageData >= 4X There is a 7.35% of reference with a coverageData >= 5X There is a 5.87% of reference with a coverageData >= 6X There is a 4.78% of reference with a coverageData >= 7X There is a 3.95% of reference with a coverageData >= 8X There is a 3.31% of reference with a coverageData >= 9X There is a 2.8% of reference with a coverageData >= 10X There is a 2.39% of reference with a coverageData >= 11X There is a 2.05% of reference with a coverageData >= 12X There is a 1.78% of reference with a coverageData >= 13X There is a 1.55% of reference with a coverageData >= 14X There is a 1.36% of reference with a coverageData >= 15X There is a 1.19% of reference with a coverageData >= 16X There is a 1.05% of reference with a coverageData >= 17X There is a 0.94% of reference with a coverageData >= 18X There is a 0.83% of reference with a coverageData >= 19X There is a 0.74% of reference with a coverageData >= 20X There is a 0.67% of reference with a coverageData >= 21X There is a 0.6% of reference with a coverageData >= 22X There is a 0.54% of reference with a coverageData >= 23X There is a 0.49% of reference with a coverageData >= 24X There is a 0.45% of reference with a coverageData >= 25X There is a 0.4% of reference with a coverageData >= 26X There is a 0.37% of reference with a coverageData >= 27X There is a 0.34% of reference with a coverageData >= 28X There is a 0.31% of reference with a coverageData >= 29X There is a 0.28% of reference with a coverageData >= 30X There is a 0.26% of reference with a coverageData >= 31X There is a 0.24% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.15% of reference with a coverageData >= 38X There is a 0.14% of reference with a coverageData >= 39X There is a 0.13% of reference with a coverageData >= 40X There is a 0.13% of reference with a coverageData >= 41X There is a 0.12% of reference with a coverageData >= 42X There is a 0.11% of reference with a coverageData >= 43X There is a 0.1% of reference with a coverageData >= 44X There is a 0.1% of reference with a coverageData >= 45X There is a 0.09% of reference with a coverageData >= 46X There is a 0.09% 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 0.07% of reference with a coverageData >= 50X There is a 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 275134885 1.1038483430699255 5.648507458830722 chr2 243199373 323028363 1.3282450485593973 4.2486410509565475 chr3 198022430 298552234 1.5076687726738836 4.055532384168235 chr4 191154276 283881042 1.4850886307141777 4.072942422809454 chr5 180915260 261295903 1.444299961208358 3.8184222681276467 chr6 171115067 228223992 1.3337457419807457 3.9965075544401345 chr7 159138663 303435140 1.9067342547674917 12.233821700825697 chr8 146364022 258381844 1.7653371400247528 4.521594377145161 chr9 141213431 133896956 0.9481885331431399 3.4633099887334744 chr10 135534747 63840413 0.47102617161339444 5.643132242612773 chr11 135006516 141409152 1.0474246443038349 3.2490052505034455 chr12 133851895 174249309 1.3018068141657613 3.9542542362289512 chr13 115169878 120437119 1.0457345365947162 3.1624401392750223 chr14 107349540 101974424 0.9499288399372741 2.9851843703842476 chr15 102531392 86158669 0.8403150227395723 2.760549732193489 chr16 90354753 56516624 0.6254969674921251 2.217419762544586 chr17 81195210 61531329 0.7578196915803285 2.9633753656079307 chr18 78077248 63630913 0.8149738192616625 2.4998693367263187 chr19 59128983 34017675 0.5753130406453972 2.948008515646824 chr20 63025520 74642483 1.184321573229384 3.768771739154851 chr21 48129895 33884643 0.7040248685354498 2.8583532981361928 chr22 51304566 17034913 0.3320350278374833 1.493322720553628 chrMT 16571 5128 0.30945627904169937 0.7329049948822796 chrX 155270560 327804096 2.111179968694645 5.578091072644025 chrY 59373566 3229590 0.05439440844769203 0.8268990838547624