BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237814.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,164,011 number of mapped reads = 2,034,986 (94.04%) number of supplementary alignments = 14,730 (0.68%) number of secondary alignments = 0 number of mapped bases = 146,128,981 bp number of sequenced bases = 146,038,587 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,964 duplication rate = 2.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.1197 >>>>>>> ACTG content number of A's = 44,949,351 bp (30.78%) number of C's = 28,524,609 bp (19.53%) number of T's = 43,514,785 bp (29.8%) number of G's = 28,805,886 bp (19.72%) number of N's = 243,956 bp (0.17%) GC percentage = 39.26% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,338,217 number of insertions = 11,278 mapped reads with insertion percentage = 0.55% number of deletions = 50,608 mapped reads with deletion percentage = 2.45% homopolymer indels = 44.1% >>>>>>> Coverage mean coverageData = 0.0472X std coverageData = 0.5526X There is a 2.73% of reference with a coverageData >= 1X There is a 1.01% of reference with a coverageData >= 2X There is a 0.45% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% 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 12185385 0.0488880828104336 1.1283564802470651 chr2 243199373 13066970 0.05372945595546416 0.5182979453579311 chr3 198022430 10943490 0.05526389106526973 0.3754174557020512 chr4 191154276 8287469 0.04335487111991154 0.36057128770396946 chr5 180915260 8186934 0.04525286589975881 0.33745705055633907 chr6 171115067 8537613 0.049893987418419446 0.39210035754605227 chr7 159138663 8444116 0.05306137327545601 0.7120916564434547 chr8 146364022 8784257 0.06001650460247669 0.5959943691666598 chr9 141213431 5968434 0.0422653423101093 0.4697623110084326 chr10 135534747 6599500 0.04869231061463523 0.534677903811954 chr11 135006516 6690205 0.04955468223474488 0.4901813518539876 chr12 133851895 6816623 0.050926608099197995 0.36079057525070024 chr13 115169878 5522085 0.0479473026792648 0.3461001607420204 chr14 107349540 4143587 0.03859901961387072 0.3295812956510349 chr15 102531392 3222874 0.03143304637861544 0.27654745038694606 chr16 90354753 3596391 0.039803008481468595 0.36064279770877766 chr17 81195210 3200553 0.03941800261370098 0.37011305806208583 chr18 78077248 3166773 0.040559485395796735 0.87842771501268 chr19 59128983 2248249 0.038022791631643654 0.66034373567195 chr20 63025520 2786455 0.044211535263810595 0.3412117524493572 chr21 48129895 2245121 0.04664712025654741 0.375777922695975 chr22 51304566 1179369 0.02298760309170143 0.23414252355626125 chrMT 16571 490810 29.618610826142056 20.658239736686863 chrX 155270560 9378117 0.06039855205004735 0.4142003340745629 chrY 59373566 437601 0.007370300109648122 0.22578013363110064