BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779373.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 = 13,469,292 number of mapped reads = 12,190,597 (90.51%) number of supplementary alignments = 176,751 (1.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,134,262 number of mapped paired reads (second in pair) = 6,056,335 number of mapped paired reads (both in pair) = 12,074,090 number of mapped paired reads (singletons) = 116,507 number of mapped bases = 962,242,489 bp number of sequenced bases = 962,034,181 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,353,888 duplication rate = 21.12% >>>>>>> Insert size mean insert size = 43,199.3019 std insert size = 1,884,834.0923 median insert size = 160 >>>>>>> Mapping quality mean mapping quality = 51.8123 >>>>>>> ACTG content number of A's = 299,081,582 bp (31.09%) number of C's = 180,934,000 bp (18.81%) number of T's = 298,060,763 bp (30.98%) number of G's = 183,748,547 bp (19.1%) number of N's = 209,289 bp (0.02%) GC percentage = 37.91% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 3,406,088 number of insertions = 107,060 mapped reads with insertion percentage = 0.87% number of deletions = 100,693 mapped reads with deletion percentage = 0.82% homopolymer indels = 47.12% >>>>>>> Coverage mean coverageData = 0.3108X std coverageData = 33.644X There is a 2.64% of reference with a coverageData >= 1X There is a 1.49% of reference with a coverageData >= 2X There is a 1% of reference with a coverageData >= 3X There is a 0.77% of reference with a coverageData >= 4X There is a 0.63% of reference with a coverageData >= 5X There is a 0.53% of reference with a coverageData >= 6X There is a 0.46% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.25% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.22% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.19% of reference with a coverageData >= 17X There is a 0.18% of reference with a coverageData >= 18X There is a 0.17% of reference with a coverageData >= 19X There is a 0.16% of reference with a coverageData >= 20X There is a 0.15% of reference with a coverageData >= 21X There is a 0.15% of reference with a coverageData >= 22X There is a 0.14% of reference with a coverageData >= 23X There is a 0.13% of reference with a coverageData >= 24X There is a 0.13% of reference with a coverageData >= 25X There is a 0.12% 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 0.11% of reference with a coverageData >= 29X There is a 0.1% of reference with a coverageData >= 30X There is a 0.1% of reference with a coverageData >= 31X There is a 0.1% of reference with a coverageData >= 32X There is a 0.09% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.08% of reference with a coverageData >= 37X There is a 0.08% of reference with a coverageData >= 38X There is a 0.08% of reference with a coverageData >= 39X There is a 0.07% of reference with a coverageData >= 40X There is a 0.07% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.07% of reference with a coverageData >= 43X There is a 0.07% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.06% 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 57604672 0.23111144826395438 24.846743021610877 chr2 243199373 72657067 0.2987551575636669 13.845169201791064 chr3 198022430 70910232 0.3580919191830946 29.005489868786945 chr4 191154276 51448210 0.2691449601681942 13.886719379098235 chr5 180915260 81897065 0.4526819075405801 66.88503347448938 chr6 171115067 60159931 0.3515758843141498 28.514964443276877 chr7 159138663 133952030 0.8417315281830664 60.525261783881014 chr8 146364022 34980290 0.2389951404860957 8.968349051658677 chr9 141213431 23501837 0.16642777413998247 4.877461009802194 chr10 135534747 23374291 0.17245976782617967 16.272704086228362 chr11 135006516 40337838 0.2987843786739893 20.975715650411924 chr12 133851895 73301629 0.5476323588844222 59.32885349179579 chr13 115169878 24905722 0.21625204812668117 28.992248483401013 chr14 107349540 46417389 0.43239485702500446 62.82896727224688 chr15 102531392 30771429 0.3001171485119406 41.98589662902639 chr16 90354753 28020317 0.3101144773203021 28.209086710436036 chr17 81195210 30742612 0.3786259312587528 40.38129141083632 chr18 78077248 20618471 0.2640778399361617 12.143816286370347 chr19 59128983 12963567 0.21924217773202695 19.989122405503363 chr20 63025520 8338536 0.13230412061653757 3.5490146513421443 chr21 48129895 4985818 0.10359087631502209 1.5917715375991341 chr22 51304566 1862599 0.03630474137526083 0.8321866536163938 chrMT 16571 330303 19.932593084303903 11.987254548017797 chrX 155270560 26046623 0.16774991344141477 17.07589879418882 chrY 59373566 2114011 0.03560525571261797 0.6579174431978222