BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779175.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 = 28,718,580 number of mapped reads = 27,561,614 (95.97%) number of supplementary alignments = 176,455 (0.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,852,695 number of mapped paired reads (second in pair) = 13,708,919 number of mapped paired reads (both in pair) = 27,290,856 number of mapped paired reads (singletons) = 270,758 number of mapped bases = 2,748,681,435 bp number of sequenced bases = 2,748,057,891 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 984,992 duplication rate = 3.23% >>>>>>> Insert size mean insert size = 86,979.9773 std insert size = 2,781,662.5579 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 53.4277 >>>>>>> ACTG content number of A's = 836,850,523 bp (30.45%) number of C's = 536,982,660 bp (19.54%) number of T's = 826,209,415 bp (30.07%) number of G's = 546,900,678 bp (19.9%) number of N's = 1,114,615 bp (0.04%) GC percentage = 39.44% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 11,266,248 number of insertions = 225,949 mapped reads with insertion percentage = 0.81% number of deletions = 278,707 mapped reads with deletion percentage = 0.99% homopolymer indels = 46.26% >>>>>>> Coverage mean coverageData = 0.8879X std coverageData = 2.1818X There is a 35.12% of reference with a coverageData >= 1X There is a 19.83% of reference with a coverageData >= 2X There is a 11.38% of reference with a coverageData >= 3X There is a 6.96% of reference with a coverageData >= 4X There is a 4.42% of reference with a coverageData >= 5X There is a 2.91% of reference with a coverageData >= 6X There is a 1.97% of reference with a coverageData >= 7X There is a 1.37% of reference with a coverageData >= 8X There is a 0.97% of reference with a coverageData >= 9X There is a 0.71% of reference with a coverageData >= 10X There is a 0.53% of reference with a coverageData >= 11X There is a 0.4% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.24% of reference with a coverageData >= 14X There is a 0.19% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% 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 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 222232160 0.8916012289493955 2.3209676267062234 chr2 243199373 173056607 0.7115832778072171 1.9911243101298617 chr3 198022430 195580969 0.9876707855771693 1.899813178685521 chr4 191154276 168238842 0.8801207355675371 1.7598626632395127 chr5 180915260 90943393 0.5026850305496617 1.2497086610667203 chr6 171115067 178116712 1.0409177585747023 1.9672656533562973 chr7 159138663 284309515 1.786552115245558 4.7224069038344485 chr8 146364022 208187051 1.4223922529267472 2.3335422354373887 chr9 141213431 129136610 0.9144782410959196 1.9911972405479963 chr10 135534747 91696136 0.6765507593414403 2.6587044313200767 chr11 135006516 167072180 1.2375119731258009 2.173025892838572 chr12 133851895 63487186 0.4743092057082942 1.3282404818911633 chr13 115169878 83365263 0.7238460650275239 1.635919605456015 chr14 107349540 107622351 1.0025413336657054 1.954902518624287 chr15 102531392 102893233 1.003529075270918 2.14561991974259 chr16 90354753 61481825 0.6804492620327345 1.487024948658434 chr17 81195210 71608674 0.8819322469884615 1.8942783268489298 chr18 78077248 52202358 0.6685988471314973 1.4824806895669427 chr19 59128983 38038429 0.6433127557766384 1.7078454547387225 chr20 63025520 74259544 1.1782456376401178 2.412313524707528 chr21 48129895 32026613 0.6654203795790538 1.537706122722336 chr22 51304566 19922867 0.3883254172737764 1.1206107122831712 chrMT 16571 749 0.04519944481322793 0.24896692178204413 chrX 155270560 131510126 0.8469739917212896 1.826456377752209 chrY 59373566 1692042 0.028498237751123118 0.47541998913830447