BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779280.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 = 11,377,640 number of mapped reads = 10,935,893 (96.12%) number of supplementary alignments = 25,870 (0.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,506,544 number of mapped paired reads (second in pair) = 5,429,349 number of mapped paired reads (both in pair) = 10,841,660 number of mapped paired reads (singletons) = 94,233 number of mapped bases = 870,219,428 bp number of sequenced bases = 870,053,336 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 149,043 duplication rate = 1.2% >>>>>>> Insert size mean insert size = 57,391.4424 std insert size = 2,255,045.2464 median insert size = 191 >>>>>>> Mapping quality mean mapping quality = 53.0237 >>>>>>> ACTG content number of A's = 266,425,455 bp (30.62%) number of C's = 167,855,027 bp (19.29%) number of T's = 264,425,259 bp (30.39%) number of G's = 171,182,333 bp (19.67%) number of N's = 165,262 bp (0.02%) GC percentage = 38.97% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 3,304,669 number of insertions = 62,849 mapped reads with insertion percentage = 0.57% number of deletions = 80,005 mapped reads with deletion percentage = 0.72% homopolymer indels = 46.18% >>>>>>> Coverage mean coverageData = 0.2811X std coverageData = 0.9048X There is a 17.78% of reference with a coverageData >= 1X There is a 6.04% of reference with a coverageData >= 2X There is a 2.22% of reference with a coverageData >= 3X There is a 0.92% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.21% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.03% 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 0.01% 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 0.01% 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 63917578 0.2564389919814884 1.1815460432956095 chr2 243199373 63927878 0.2628620181516669 0.7057903469508495 chr3 198022430 49839844 0.2516878719244078 0.6774424337614022 chr4 191154276 76669497 0.40108700995001545 0.8928796005522054 chr5 180915260 51514695 0.28474488553370236 0.7194675876779151 chr6 171115067 50925561 0.29761003453892226 0.7497468290802068 chr7 159138663 85546033 0.5375565647425352 1.8123054408242794 chr8 146364022 71914610 0.49134076132452825 0.9778177639574519 chr9 141213431 33850947 0.23971478322058473 0.7153864078980138 chr10 135534747 25022991 0.18462417611625453 1.3703795416770959 chr11 135006516 31882467 0.2361550238064065 0.6733255883534912 chr12 133851895 29496942 0.22036999924431402 0.6239912892344239 chr13 115169878 27619491 0.23981523189596501 0.6574342980120633 chr14 107349540 24989954 0.23279050846421884 0.6683665050597987 chr15 102531392 20479424 0.1997380860683136 0.6242941319967202 chr16 90354753 16446158 0.18201762999673077 0.5916767641989142 chr17 81195210 15090922 0.18585975699798055 0.6906728913285166 chr18 78077248 25138955 0.3219754236214883 0.7931139073321124 chr19 59128983 8530519 0.14426967228575535 0.7489371169522944 chr20 63025520 19173090 0.30421153209049284 0.7848100545989467 chr21 48129895 8567608 0.17801011201042513 0.5796164000978294 chr22 51304566 4361685 0.08501553253564215 0.39346552240244764 chrMT 16571 868 0.05238066501719872 0.26063040605972504 chrX 155270560 64749058 0.41700795050909845 0.9461882666698774 chrY 59373566 562653 0.009476489924826142 0.13847574797393075