BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094119.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 398,342 number of mapped reads = 343,704 (86.28%) number of supplementary alignments = 3,668 (0.92%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 172,407 number of mapped paired reads (second in pair) = 171,297 number of mapped paired reads (both in pair) = 341,008 number of mapped paired reads (singletons) = 2,696 number of mapped bases = 50,023,318 bp number of sequenced bases = 49,983,271 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 343,550 duplication rate = 44.77% >>>>>>> Insert size mean insert size = 18,099.794 std insert size = 1,323,225.2532 median insert size = 231 >>>>>>> Mapping quality mean mapping quality = 16.0618 >>>>>>> ACTG content number of A's = 13,539,813 bp (27.09%) number of C's = 10,776,407 bp (21.56%) number of T's = 14,313,978 bp (28.64%) number of G's = 11,352,476 bp (22.71%) number of N's = 597 bp (0%) GC percentage = 44.27% >>>>>>> Mismatches and indels general error rate = 0.016 number of mismatches = 762,962 number of insertions = 24,673 mapped reads with insertion percentage = 7.08% number of deletions = 31,881 mapped reads with deletion percentage = 9.07% homopolymer indels = 62.76% >>>>>>> Coverage mean coverageData = 0.0162X std coverageData = 27.3774X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 10964 4.398785429706111E-5 0.023578646755511506 chr2 243199373 224951 9.24965378097418E-4 0.8730240898025042 chr3 198022430 7132 3.601612201203672E-5 0.01349123644721558 chr4 191154276 8110 4.2426463952080255E-5 0.01578126601564129 chr5 180915260 8478 4.686171857476257E-5 0.019788912433563073 chr6 171115067 9984 5.83467030404751E-5 0.030099754357628898 chr7 159138663 63948 4.018382383921373E-4 0.593294179606679 chr8 146364022 3831390 0.026177129786717667 9.057169486103518 chr9 141213431 5091 3.6051811530590176E-5 0.009268068276896534 chr10 135534747 6493 4.790653425575067E-5 0.013499313959786536 chr11 135006516 7509 5.561953765253819E-5 0.029322472285063145 chr12 133851895 5804 4.336135846265008E-5 0.012304040136010419 chr13 115169878 3687 3.201357910616177E-5 0.010205790497184909 chr14 107349540 4678 4.3577271034417105E-5 0.023829869367099507 chr15 102531392 5426 5.2920377790247885E-5 0.014693934225494275 chr16 90354753 9550 1.056944951196978E-4 0.04302715368672677 chr17 81195210 67173 8.273024972778566E-4 0.20749514365011648 chr18 78077248 18129 2.3219312238054293E-4 0.10386883970214479 chr19 59128983 12499 2.1138533703513892E-4 0.19773143131290896 chr20 63025520 2237 3.5493558799673526E-5 0.007215055235963767 chr21 48129895 2555 5.3085509536224836E-5 0.017249530200653607 chr22 51304566 2473 4.820233739039913E-5 0.027138198774793107 chrMT 16571 45596026 2751.555488504013 11477.007973729942 chrX 155270560 105398 6.788022146632304E-4 0.09070948516446056 chrY 59373566 3633 6.118884622830302E-5 0.014970627896967131