BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779007.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 = 20,702,358 number of mapped reads = 20,080,507 (97%) number of supplementary alignments = 113,855 (0.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,144,844 number of mapped paired reads (second in pair) = 9,935,663 number of mapped paired reads (both in pair) = 19,803,992 number of mapped paired reads (singletons) = 276,515 number of mapped bases = 2,006,122,956 bp number of sequenced bases = 2,005,639,886 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 438,555 duplication rate = 1.89% >>>>>>> Insert size mean insert size = 75,814.0959 std insert size = 2,635,019.8539 median insert size = 274 >>>>>>> Mapping quality mean mapping quality = 53.6664 >>>>>>> ACTG content number of A's = 614,147,267 bp (30.62%) number of C's = 386,498,604 bp (19.27%) number of T's = 611,167,027 bp (30.47%) number of G's = 393,152,737 bp (19.6%) number of N's = 674,251 bp (0.03%) GC percentage = 38.87% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 9,977,788 number of insertions = 176,804 mapped reads with insertion percentage = 0.87% number of deletions = 217,162 mapped reads with deletion percentage = 1.06% homopolymer indels = 47.1% >>>>>>> Coverage mean coverageData = 0.648X std coverageData = 1.606X There is a 33.42% of reference with a coverageData >= 1X There is a 14.94% of reference with a coverageData >= 2X There is a 7.12% of reference with a coverageData >= 3X There is a 3.62% of reference with a coverageData >= 4X There is a 1.95% of reference with a coverageData >= 5X There is a 1.1% of reference with a coverageData >= 6X There is a 0.65% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.26% of reference with a coverageData >= 9X There is a 0.17% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% 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 149794009 0.6009774755987468 1.8114051036762826 chr2 243199373 160846269 0.6613761664591133 1.3883523291467297 chr3 198022430 141907277 0.7166222381979658 1.275813292022684 chr4 191154276 135341168 0.7080206147206458 1.2762624076614675 chr5 180915260 135029317 0.7463677580321306 1.3062193137803868 chr6 171115067 122254810 0.7144596448657557 1.308940355696076 chr7 159138663 189017067 1.1877507541960435 3.8999576615483864 chr8 146364022 147150495 1.0053734038546713 1.5917002283557742 chr9 141213431 77663583 0.5499730616983592 1.2395806516725127 chr10 135534747 48787377 0.35996213576139263 1.9029913404847085 chr11 135006516 82125757 0.6083095796650289 1.1924031061221416 chr12 133851895 92248741 0.6891851699223235 1.3077192002747116 chr13 115169878 64176149 0.5572303289233318 1.1536465984649362 chr14 107349540 54802191 0.5105023365726579 1.1139883741417391 chr15 102531392 46218619 0.45077530011491507 1.098852771037939 chr16 90354753 34039048 0.3767267008078701 0.9273359720760768 chr17 81195210 32381418 0.39880946178967946 1.063540589527763 chr18 78077248 52756238 0.6756928471659247 1.2933541986771395 chr19 59128983 23392608 0.39561999569652667 1.1841333267180043 chr20 63025520 40412031 0.6412010722005943 1.3093138523000256 chr21 48129895 24342792 0.5057728050310519 1.1584950755700265 chr22 51304566 10216854 0.19914122263503797 0.6669667597493034 chrMT 16571 793 0.04785468589704906 0.2481172777959055 chrX 155270560 139907994 0.9010593766133129 1.5998358193228301 chrY 59373566 1310351 0.022069602489431073 0.32654450196618384