BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779301.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 = 31,822,656 number of mapped reads = 30,224,886 (94.98%) number of supplementary alignments = 75,541 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,234,844 number of mapped paired reads (second in pair) = 14,990,042 number of mapped paired reads (both in pair) = 29,928,852 number of mapped paired reads (singletons) = 296,034 number of mapped bases = 2,405,798,909 bp number of sequenced bases = 2,405,326,156 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,648,182 duplication rate = 7.54% >>>>>>> Insert size mean insert size = 36,162.569 std insert size = 1,787,421.417 median insert size = 227 >>>>>>> Mapping quality mean mapping quality = 52.933 >>>>>>> ACTG content number of A's = 739,422,457 bp (30.74%) number of C's = 459,907,306 bp (19.12%) number of T's = 736,201,904 bp (30.61%) number of G's = 469,161,151 bp (19.51%) number of N's = 633,338 bp (0.03%) GC percentage = 38.63% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 8,799,326 number of insertions = 181,530 mapped reads with insertion percentage = 0.59% number of deletions = 227,099 mapped reads with deletion percentage = 0.74% homopolymer indels = 46.73% >>>>>>> Coverage mean coverageData = 0.7771X std coverageData = 3.7632X There is a 19.82% of reference with a coverageData >= 1X There is a 11.3% of reference with a coverageData >= 2X There is a 7.66% of reference with a coverageData >= 3X There is a 5.65% of reference with a coverageData >= 4X There is a 4.36% of reference with a coverageData >= 5X There is a 3.48% of reference with a coverageData >= 6X There is a 2.84% of reference with a coverageData >= 7X There is a 2.36% of reference with a coverageData >= 8X There is a 1.99% of reference with a coverageData >= 9X There is a 1.7% of reference with a coverageData >= 10X There is a 1.46% of reference with a coverageData >= 11X There is a 1.27% of reference with a coverageData >= 12X There is a 1.11% of reference with a coverageData >= 13X There is a 0.98% of reference with a coverageData >= 14X There is a 0.86% of reference with a coverageData >= 15X There is a 0.77% of reference with a coverageData >= 16X There is a 0.69% of reference with a coverageData >= 17X There is a 0.61% of reference with a coverageData >= 18X There is a 0.55% of reference with a coverageData >= 19X There is a 0.5% of reference with a coverageData >= 20X There is a 0.45% of reference with a coverageData >= 21X There is a 0.41% of reference with a coverageData >= 22X There is a 0.38% of reference with a coverageData >= 23X There is a 0.34% of reference with a coverageData >= 24X There is a 0.32% of reference with a coverageData >= 25X There is a 0.29% of reference with a coverageData >= 26X There is a 0.27% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.16% of reference with a coverageData >= 34X There is a 0.15% of reference with a coverageData >= 35X There is a 0.14% of reference with a coverageData >= 36X There is a 0.13% of reference with a coverageData >= 37X There is a 0.12% of reference with a coverageData >= 38X There is a 0.12% of reference with a coverageData >= 39X There is a 0.11% 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 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.06% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 177560717 0.7123782331519246 4.554012166405712 chr2 243199373 192972856 0.793475960153894 3.1385195093568274 chr3 198022430 162637367 0.8213078033634876 3.1322427397943433 chr4 191154276 166264984 0.8697947410812824 3.228161260720261 chr5 180915260 147888689 0.8174472899632679 3.030820077911242 chr6 171115067 138421542 0.8089383619269482 3.279786198025148 chr7 159138663 232144917 1.4587587492801797 8.892896781657637 chr8 146364022 197373571 1.3485115283317373 4.283888772932628 chr9 141213431 93707455 0.6635874104638106 2.600142912258492 chr10 135534747 53691587 0.39614628859712264 2.4537439463105195 chr11 135006516 112534996 0.8335523301704933 3.0117692764967146 chr12 133851895 96008659 0.7172753064123597 2.9690440998163883 chr13 115169878 85451626 0.7419615917280037 2.941134574888 chr14 107349540 76395615 0.7116529330260754 3.036144313341286 chr15 102531392 56261923 0.548728754214124 2.6761725583727776 chr16 90354753 36828016 0.407593566217817 2.2201577275931963 chr17 81195210 34969643 0.43068603431162994 2.0625380276381824 chr18 78077248 62432930 0.7996302584845204 3.1970617953415803 chr19 59128983 24232250 0.4098201722833623 2.2713574255311677 chr20 63025520 45884392 0.728028773106513 2.9409047218089923 chr21 48129895 21695647 0.45077278892879363 1.9429844953961577 chr22 51304566 16278851 0.3172982888111752 4.877738270511851 chrMT 16571 2372 0.14314163297326654 0.48391345445596035 chrX 155270560 172209840 1.1090952463879824 4.063220408893432 chrY 59373566 1948464 0.03281702837252524 0.5163584435950349