BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927004.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 24,977,928 number of mapped reads = 24,576,413 (98.39%) number of supplementary alignments = 358,951 (1.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,315,544 number of mapped paired reads (second in pair) = 12,260,869 number of mapped paired reads (both in pair) = 24,327,208 number of mapped paired reads (singletons) = 249,205 number of mapped bases = 2,306,578,759 bp number of sequenced bases = 2,304,799,520 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,724,842 duplication rate = 5.57% >>>>>>> Insert size mean insert size = 147,488.8809 std insert size = 3,755,817.8628 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 53.4283 >>>>>>> ACTG content number of A's = 667,738,352 bp (28.97%) number of C's = 448,491,875 bp (19.46%) number of T's = 678,157,879 bp (29.42%) number of G's = 510,151,760 bp (22.13%) number of N's = 259,654 bp (0.01%) GC percentage = 41.59% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 20,824,025 number of insertions = 387,482 mapped reads with insertion percentage = 1.55% number of deletions = 1,247,015 mapped reads with deletion percentage = 4.94% homopolymer indels = 53.14% >>>>>>> Coverage mean coverageData = 0.7451X std coverageData = 2.7995X There is a 31.59% of reference with a coverageData >= 1X There is a 17% of reference with a coverageData >= 2X There is a 9.53% of reference with a coverageData >= 3X There is a 5.64% of reference with a coverageData >= 4X There is a 3.44% of reference with a coverageData >= 5X There is a 2.15% of reference with a coverageData >= 6X There is a 1.37% of reference with a coverageData >= 7X There is a 0.89% of reference with a coverageData >= 8X There is a 0.58% of reference with a coverageData >= 9X There is a 0.39% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.18% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 187756643 0.7532845545046807 3.8206512591179314 chr2 243199373 202063168 0.830853984150691 4.626526808928674 chr3 198022430 157424873 0.7949850580058027 1.5998684567838233 chr4 191154276 144308832 0.7549338420240205 2.008745681303481 chr5 180915260 140958428 0.7791406208630494 1.571797877897668 chr6 171115067 136830530 0.7996404548057712 2.473107602392604 chr7 159138663 118516438 0.744736921661834 2.400482158258843 chr8 146364022 119994541 0.8198363187915129 1.8425711170017642 chr9 141213431 94498413 0.6691885632323458 3.3725623855495703 chr10 135534747 112314654 0.8286779330469404 5.324162982965766 chr11 135006516 110340611 0.8172984109892888 2.677834576514448 chr12 133851895 104186286 0.7783698990589561 1.6198968636234057 chr13 115169878 73271183 0.6362009257316397 1.4286739939191198 chr14 107349540 69982695 0.6519142513326094 1.5011595307021375 chr15 102531392 67858238 0.6618288962662284 1.5238003208034447 chr16 90354753 69261853 0.7665546161141075 3.242365680940647 chr17 81195210 55971509 0.6893449625907735 1.9887681431685025 chr18 78077248 63077940 0.8078914359276598 3.0875542773325413 chr19 59128983 33509723 0.5667224650219335 2.3708940162695136 chr20 63025520 51154704 0.8116506456432252 1.7387228428946795 chr21 48129895 29131931 0.6052772606298019 2.32765087869299 chr22 51304566 25568690 0.4983706518441263 1.3712847799357517 chrMT 16571 86032 5.191720475529539 5.069933715447651 chrX 155270560 134913282 0.8688915786740256 1.9339975445289477 chrY 59373566 3597562 0.06059198128675647 1.9470628778319476