BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084858.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,308,651 number of mapped reads = 1,921,634 (83.24%) number of supplementary alignments = 17,718 (0.77%) number of secondary alignments = 0 number of mapped bases = 127,465,873 bp number of sequenced bases = 127,419,951 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 116,561 duplication rate = 5.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7496 >>>>>>> ACTG content number of A's = 35,121,078 bp (27.56%) number of C's = 23,522,231 bp (18.46%) number of T's = 40,453,571 bp (31.75%) number of G's = 28,304,791 bp (22.21%) number of N's = 18,280 bp (0.01%) GC percentage = 40.67% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,085,336 number of insertions = 9,605 mapped reads with insertion percentage = 0.5% number of deletions = 26,285 mapped reads with deletion percentage = 1.35% homopolymer indels = 47.68% >>>>>>> Coverage mean coverageData = 0.0412X std coverageData = 0.3181X There is a 3.43% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 9925982 0.039823298975852905 0.5630645565618417 chr2 243199373 11256253 0.04628405435897238 0.3180061042576739 chr3 198022430 8947859 0.04518608826282962 0.24576935639099887 chr4 191154276 8448355 0.04419652637014513 0.24932868853392753 chr5 180915260 7447112 0.04116353700622048 0.23648531950589283 chr6 171115067 7687970 0.044928656107179624 0.2538061598711199 chr7 159138663 6770044 0.04254179262521516 0.27327728418563685 chr8 146364022 6467451 0.04418743699185856 0.46033017125461007 chr9 141213431 5717336 0.040487197000404304 0.2892912860529465 chr10 135534747 6339645 0.046775053189865766 0.3068926862530985 chr11 135006516 5822665 0.04312877016987832 0.2802516205447708 chr12 133851895 5665278 0.04232497418135171 0.2417764137038083 chr13 115169878 4022357 0.034925425552677934 0.2168714365092654 chr14 107349540 4021291 0.03745978790407486 0.23852287977706482 chr15 102531392 3591004 0.035023458961719746 0.21823942348164832 chr16 90354753 3408105 0.03771915573716415 0.2358658017276717 chr17 81195210 3214224 0.03958637461495573 0.24065394582615213 chr18 78077248 3212139 0.041140525342286655 0.4903949453986498 chr19 59128983 2345830 0.039673099062096165 0.39641653020102763 chr20 63025520 2402277 0.03811594097121293 0.23438919904076141 chr21 48129895 1542487 0.03204841814011853 0.2178219696263395 chr22 51304566 1373772 0.026776797994938695 0.19000037251195986 chrMT 16571 270305 16.311930480960715 8.293990071384803 chrX 155270560 7255742 0.04672966980991117 0.2605610939871063 chrY 59373566 310390 0.005227747310983477 0.11399598116769376