BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779158.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 = 16,798,892 number of mapped reads = 15,623,879 (93.01%) number of supplementary alignments = 94,941 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,889,670 number of mapped paired reads (second in pair) = 7,734,209 number of mapped paired reads (both in pair) = 15,376,468 number of mapped paired reads (singletons) = 247,411 number of mapped bases = 1,559,994,121 bp number of sequenced bases = 1,559,641,615 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 441,768 duplication rate = 2.49% >>>>>>> Insert size mean insert size = 63,031.2235 std insert size = 2,421,518.782 median insert size = 225 >>>>>>> Mapping quality mean mapping quality = 53.6101 >>>>>>> ACTG content number of A's = 480,996,798 bp (30.84%) number of C's = 297,195,703 bp (19.06%) number of T's = 478,943,676 bp (30.71%) number of G's = 301,874,972 bp (19.36%) number of N's = 630,466 bp (0.04%) GC percentage = 38.41% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 6,480,564 number of insertions = 128,824 mapped reads with insertion percentage = 0.81% number of deletions = 158,755 mapped reads with deletion percentage = 1% homopolymer indels = 46.82% >>>>>>> Coverage mean coverageData = 0.5039X std coverageData = 1.654X There is a 22.18% of reference with a coverageData >= 1X There is a 10.59% of reference with a coverageData >= 2X There is a 5.7% of reference with a coverageData >= 3X There is a 3.43% of reference with a coverageData >= 4X There is a 2.21% of reference with a coverageData >= 5X There is a 1.5% of reference with a coverageData >= 6X There is a 1.05% of reference with a coverageData >= 7X There is a 0.76% of reference with a coverageData >= 8X There is a 0.57% of reference with a coverageData >= 9X There is a 0.43% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.21% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% 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 115323769 0.4626819726158275 1.7952330944115504 chr2 243199373 135667393 0.5578443370411157 1.7430430321422818 chr3 198022430 130403128 0.6585270567581663 1.7949582335306125 chr4 191154276 119866820 0.6270684732158437 1.6477729995061816 chr5 180915260 101369826 0.5603166145299185 1.6537432732958763 chr6 171115067 104797203 0.6124370275353952 1.6301459784165415 chr7 159138663 88600640 0.5567511899983727 1.620969983296034 chr8 146364022 93705467 0.6402220007318465 1.6374422448271297 chr9 141213431 58621630 0.41512786414770986 1.3877207263335654 chr10 135534747 58633040 0.4326052270566455 2.8474460053322432 chr11 135006516 68369622 0.5064172013741914 1.451442462842579 chr12 133851895 82713552 0.6179483077172722 1.8080166800812107 chr13 115169878 50546098 0.43888296903466373 1.2743166600548652 chr14 107349540 45274617 0.4217495203053502 1.4075612090367926 chr15 102531392 39190362 0.382227932690117 1.3696108314263982 chr16 90354753 25256503 0.27952600346325995 0.9847983505526982 chr17 81195210 22269711 0.2742737040768784 1.1128523524162934 chr18 78077248 39186036 0.5018880276108092 1.482133696929121 chr19 59128983 13042248 0.22057284496166626 1.1851498736479338 chr20 63025520 25229307 0.40030303597653777 1.2635185579665045 chr21 48129895 17530502 0.36423312371655914 1.1021553091838667 chr22 51304566 7314727 0.14257458098368866 0.6341423669195343 chrMT 16571 386 0.02329370587170358 0.1836685923160589 chrX 155270560 116144602 0.7480143177174089 2.017634977334581 chrY 59373566 936932 0.015780288487304266 0.27048416613513054