BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472710.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 16,744,586 number of mapped reads = 16,637,260 (99.36%) number of supplementary alignments = 69,461 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,335,043 number of mapped paired reads (second in pair) = 8,302,217 number of mapped paired reads (both in pair) = 16,573,578 number of mapped paired reads (singletons) = 63,682 number of mapped bases = 1,640,031,565 bp number of sequenced bases = 1,639,809,131 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,615,325 duplication rate = 46.06% >>>>>>> Insert size mean insert size = 22,410.4919 std insert size = 1,433,779.7091 median insert size = 216 >>>>>>> Mapping quality mean mapping quality = 54.8232 >>>>>>> ACTG content number of A's = 455,381,668 bp (27.77%) number of C's = 367,471,945 bp (22.41%) number of T's = 451,755,261 bp (27.55%) number of G's = 364,872,506 bp (22.25%) number of N's = 327,751 bp (0.02%) GC percentage = 44.66% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 8,724,653 number of insertions = 86,537 mapped reads with insertion percentage = 0.51% number of deletions = 83,181 mapped reads with deletion percentage = 0.49% homopolymer indels = 45.55% >>>>>>> Coverage mean coverageData = 0.5298X std coverageData = 29.3616X There is a 4.27% of reference with a coverageData >= 1X There is a 2.09% of reference with a coverageData >= 2X There is a 1% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.28% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.25% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.22% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.21% of reference with a coverageData >= 17X There is a 0.2% of reference with a coverageData >= 18X There is a 0.2% of reference with a coverageData >= 19X There is a 0.19% of reference with a coverageData >= 20X There is a 0.19% of reference with a coverageData >= 21X There is a 0.18% of reference with a coverageData >= 22X There is a 0.18% of reference with a coverageData >= 23X There is a 0.17% of reference with a coverageData >= 24X There is a 0.17% of reference with a coverageData >= 25X There is a 0.17% of reference with a coverageData >= 26X There is a 0.16% of reference with a coverageData >= 27X There is a 0.16% of reference with a coverageData >= 28X There is a 0.16% of reference with a coverageData >= 29X There is a 0.15% of reference with a coverageData >= 30X There is a 0.15% of reference with a coverageData >= 31X There is a 0.15% of reference with a coverageData >= 32X There is a 0.15% of reference with a coverageData >= 33X There is a 0.14% of reference with a coverageData >= 34X There is a 0.14% of reference with a coverageData >= 35X There is a 0.14% of reference with a coverageData >= 36X There is a 0.14% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.13% of reference with a coverageData >= 39X There is a 0.13% of reference with a coverageData >= 40X There is a 0.13% of reference with a coverageData >= 41X There is a 0.13% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.12% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 90518439 0.3631623409275277 15.575509810526897 chr2 243199373 94989787 0.39058401273098675 18.45990568710131 chr3 198022430 267730891 1.35202305617601 49.510810076448216 chr4 191154276 73440916 0.384197086964458 51.20247428744417 chr5 180915260 68593766 0.3791485914455199 15.888657767037605 chr6 171115067 60240364 0.35204593643410725 10.749686084172163 chr7 159138663 159231468 1.0005831706654467 40.42639503307148 chr8 146364022 60399340 0.4126652108535252 17.371237332124984 chr9 141213431 143420639 1.0156302979424103 35.42116519603354 chr10 135534747 20238779 0.14932539033698863 8.88189648432187 chr11 135006516 38000308 0.28147017733573687 11.008770176100528 chr12 133851895 53830498 0.4021646312889332 15.650422242268384 chr13 115169878 32939139 0.2860048093478053 12.678469267412847 chr14 107349540 80703334 0.7517809019023277 31.24019226644987 chr15 102531392 35452877 0.3457758283433819 18.35819904884116 chr16 90354753 34307561 0.37969846478358477 12.051596619293758 chr17 81195210 61581427 0.7584366984210029 34.17673413080451 chr18 78077248 50000898 0.6404029250621128 52.218053130521355 chr19 59128983 39117186 0.6615568882691589 33.65037116241379 chr20 63025520 20127765 0.3193589676055033 12.442037444379407 chr21 48129895 5816890 0.12085814855818822 8.785350918980985 chr22 51304566 12352071 0.24075968209145363 11.094172497456 chrMT 16571 1532 0.09245066682759037 0.33614059584676675 chrX 155270560 134226402 0.8644678166936475 48.55802265943928 chrY 59373566 2769288 0.0466417664723052 2.3448310746099468