BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779205.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 = 7,988,722 number of mapped reads = 7,717,790 (96.61%) number of supplementary alignments = 28,098 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,912,166 number of mapped paired reads (second in pair) = 3,805,624 number of mapped paired reads (both in pair) = 7,596,288 number of mapped paired reads (singletons) = 121,502 number of mapped bases = 613,140,769 bp number of sequenced bases = 613,008,473 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,437 duplication rate = 0.84% >>>>>>> Insert size mean insert size = 55,766.8265 std insert size = 2,276,071.7996 median insert size = 277 >>>>>>> Mapping quality mean mapping quality = 53.3398 >>>>>>> ACTG content number of A's = 184,566,102 bp (30.11%) number of C's = 120,703,744 bp (19.69%) number of T's = 184,043,753 bp (30.02%) number of G's = 123,582,104 bp (20.16%) number of N's = 112,770 bp (0.02%) GC percentage = 39.85% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 3,050,030 number of insertions = 54,298 mapped reads with insertion percentage = 0.7% number of deletions = 63,717 mapped reads with deletion percentage = 0.81% homopolymer indels = 47.03% >>>>>>> Coverage mean coverageData = 0.1981X std coverageData = 0.8239X There is a 15.32% of reference with a coverageData >= 1X There is a 3.12% of reference with a coverageData >= 2X There is a 0.68% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% 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 54908972 0.22029622947258373 1.8274587266489808 chr2 243199373 40672668 0.16724001998146598 0.5050329277349709 chr3 198022430 38701463 0.195439794370769 0.5016307922133908 chr4 191154276 39090222 0.2044956713393113 0.5141022595851675 chr5 180915260 38732605 0.21409252597044606 0.5275642635594755 chr6 171115067 32435623 0.1895544534368794 0.5431085299165366 chr7 159138663 59841550 0.3760340125516827 1.5073887057782571 chr8 146364022 44426301 0.3035329337970775 0.6560952369026488 chr9 141213431 22742384 0.16104972337935758 0.5574213816787515 chr10 135534747 16785168 0.12384402060380871 0.8099492165574629 chr11 135006516 27848465 0.20627496972072074 0.551913339258334 chr12 133851895 25559896 0.1909565494011123 0.5010749063103561 chr13 115169878 20592331 0.1787996250200074 0.48773148265083377 chr14 107349540 16877261 0.15721782319700672 0.4586350347171125 chr15 102531392 15045329 0.14673875684824408 0.44378523863508607 chr16 90354753 13133151 0.14535097008123082 0.4502292936752881 chr17 81195210 14346842 0.17669566960908162 0.8190579924575636 chr18 78077248 19494710 0.24968490180391603 0.6881625066463641 chr19 59128983 9571863 0.1618810693902853 1.241501832017135 chr20 63025520 15591688 0.24738689978281814 0.5848429797847645 chr21 48129895 8019441 0.16662078735056454 0.4817674041321229 chr22 51304566 6103722 0.11897034661593278 0.40414911037934975 chrMT 16571 480 0.028966266368957817 0.167711722254589 chrX 155270560 32149847 0.20705693983457005 0.5606221862870007 chrY 59373566 468787 0.007895550690015823 0.1294329584777584