BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926944.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 11,572,714 number of mapped reads = 11,297,218 (97.62%) number of supplementary alignments = 146,799 (1.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,673,595 number of mapped paired reads (second in pair) = 5,623,623 number of mapped paired reads (both in pair) = 11,159,802 number of mapped paired reads (singletons) = 137,416 number of mapped bases = 1,048,958,440 bp number of sequenced bases = 1,048,157,539 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 601,436 duplication rate = 4.27% >>>>>>> Insert size mean insert size = 142,347.4511 std insert size = 3,763,543.4493 median insert size = 188 >>>>>>> Mapping quality mean mapping quality = 53.3321 >>>>>>> ACTG content number of A's = 300,307,617 bp (28.65%) number of C's = 206,414,095 bp (19.69%) number of T's = 304,964,875 bp (29.1%) number of G's = 236,415,416 bp (22.56%) number of N's = 55,536 bp (0.01%) GC percentage = 42.25% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 9,419,214 number of insertions = 176,289 mapped reads with insertion percentage = 1.53% number of deletions = 557,989 mapped reads with deletion percentage = 4.81% homopolymer indels = 52.97% >>>>>>> Coverage mean coverageData = 0.3388X std coverageData = 1.4561X There is a 19.3% of reference with a coverageData >= 1X There is a 7.92% of reference with a coverageData >= 2X There is a 3.26% of reference with a coverageData >= 3X There is a 1.49% of reference with a coverageData >= 4X There is a 0.7% of reference with a coverageData >= 5X There is a 0.34% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.05% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% 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% 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 84410096 0.33865550930763777 1.8461431740991154 chr2 243199373 90709186 0.37298281192525934 2.805861940277061 chr3 198022430 70801165 0.35754113814278515 0.8933091751809602 chr4 191154276 61289545 0.3206286894675587 1.1566579925478488 chr5 180915260 65551738 0.3623339346830113 0.8871138550540417 chr6 171115067 59376084 0.34699506619133663 1.026601619350009 chr7 159138663 54783218 0.34424832386583515 1.0983737806084475 chr8 146364022 53311360 0.36423814590172987 0.9844670187945969 chr9 141213431 44273340 0.31352074435469246 1.5219052031354618 chr10 135534747 49803093 0.3674562730397099 1.9613424098479741 chr11 135006516 51285749 0.37987610168386243 1.7522581962295052 chr12 133851895 46277285 0.3457350006139248 0.8951815094806326 chr13 115169878 31985995 0.27772882593485076 0.7833324101614039 chr14 107349540 32974501 0.30716946714443305 0.8604540699143712 chr15 102531392 32727104 0.31919106296733 0.8722268906423828 chr16 90354753 33803837 0.3741235062642471 1.9541787997326845 chr17 81195210 26531495 0.3267618249894298 1.0964249593605533 chr18 78077248 28682446 0.3673598485438421 1.6624539992514649 chr19 59128983 17177112 0.29050240894554197 1.2035189433535267 chr20 63025520 24970702 0.39619985681990405 0.9915255939653979 chr21 48129895 13645667 0.2835174894937959 1.0319847453889277 chr22 51304566 12943234 0.25228230173509314 0.7869640083045193 chrMT 16571 102353 6.176633878462374 5.560637640683766 chrX 155270560 59920042 0.3859072962704585 1.0671535600095792 chrY 59373566 1622093 0.027320120876687785 0.9594962334412909