BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617648.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,055,665 (93.92%) number of supplementary alignments = 140,158 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,058,712 number of mapped paired reads (second in pair) = 14,996,953 number of mapped paired reads (both in pair) = 29,417,256 number of mapped paired reads (singletons) = 638,409 number of mapped bases = 2,916,268,891 bp number of sequenced bases = 2,914,505,737 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,877,273 duplication rate = 10.71% >>>>>>> Insert size mean insert size = 34,024.9527 std insert size = 1,698,200.2995 median insert size = 224 >>>>>>> Mapping quality mean mapping quality = 52.6466 >>>>>>> ACTG content number of A's = 867,947,484 bp (29.78%) number of C's = 581,432,950 bp (19.95%) number of T's = 865,955,524 bp (29.71%) number of G's = 597,196,660 bp (20.49%) number of N's = 1,973,119 bp (0.07%) GC percentage = 40.44% >>>>>>> Mismatches and indels general error rate = 0.0153 number of mismatches = 43,545,339 number of insertions = 453,681 mapped reads with insertion percentage = 1.48% number of deletions = 1,068,370 mapped reads with deletion percentage = 3.48% homopolymer indels = 47.77% >>>>>>> Coverage mean coverageData = 0.942X std coverageData = 10.51X There is a 33.22% of reference with a coverageData >= 1X There is a 19.19% of reference with a coverageData >= 2X There is a 11.7% of reference with a coverageData >= 3X There is a 7.46% of reference with a coverageData >= 4X There is a 4.9% of reference with a coverageData >= 5X There is a 3.32% of reference with a coverageData >= 6X There is a 2.29% of reference with a coverageData >= 7X There is a 1.63% of reference with a coverageData >= 8X There is a 1.18% of reference with a coverageData >= 9X There is a 0.87% of reference with a coverageData >= 10X There is a 0.65% of reference with a coverageData >= 11X There is a 0.5% of reference with a coverageData >= 12X There is a 0.39% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 178840537 0.717512904411179 10.067022063303092 chr2 243199373 301095843 1.238061756845072 12.019069865879597 chr3 198022430 244191700 1.2331517192269583 2.460670141320975 chr4 191154276 163225929 0.8538962999708152 8.259801600855283 chr5 180915260 193154909 1.0676540442193765 2.3185849190079604 chr6 171115067 141243838 0.8254319182775413 5.740646390150353 chr7 159138663 228357740 1.4349607800839699 13.47275274739478 chr8 146364022 129862733 0.8872585709622 4.070204581618916 chr9 141213431 119610803 0.8470214352344431 20.43928433692771 chr10 135534747 123454408 0.9108690629717263 21.191091681748404 chr11 135006516 160527581 1.1890358017978926 11.736987592277517 chr12 133851895 124668788 0.9313935226692158 2.1352969704993274 chr13 115169878 125186981 1.0869767614063115 2.272041240090589 chr14 107349540 83434534 0.7772230230329817 2.466299166080136 chr15 102531392 62279675 0.6074205546726607 1.5753059119526938 chr16 90354753 80734165 0.8935242731503013 16.643527792041578 chr17 81195210 71826246 0.884611863187496 12.745791721264562 chr18 78077248 53753196 0.6884617142243538 17.990343707653647 chr19 59128983 30947289 0.5233861201367187 6.065073669210766 chr20 63025520 78621505 1.2474550785142273 3.044892302625123 chr21 48129895 42588736 0.8848707440562669 4.347726802185153 chr22 51304566 18686122 0.3642194731751556 1.2532302368114603 chrMT 16571 3082729 186.0315611610645 128.50167918823394 chrX 155270560 145168333 0.9349379109600686 4.336831378498782 chrY 59373566 11724571 0.19747122818932586 17.233509588895032