BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504664.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 217,581,292 number of mapped reads = 216,714,616 (99.6%) number of supplementary alignments = 2,932,065 (1.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 108,503,001 number of mapped paired reads (second in pair) = 108,211,615 number of mapped paired reads (both in pair) = 216,332,246 number of mapped paired reads (singletons) = 382,370 number of mapped bases = 20,204,101,676 bp number of sequenced bases = 20,198,906,487 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 134,869,804 duplication rate = 35.13% >>>>>>> Insert size mean insert size = 37,306.6943 std insert size = 1,808,533.3726 median insert size = 146 >>>>>>> Mapping quality mean mapping quality = 51.3279 >>>>>>> ACTG content number of A's = 6,076,612,648 bp (30.08%) number of C's = 3,999,504,634 bp (19.8%) number of T's = 6,145,727,342 bp (30.43%) number of G's = 3,960,365,811 bp (19.61%) number of N's = 16,696,052 bp (0.08%) GC percentage = 39.41% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 106,119,598 number of insertions = 2,259,361 mapped reads with insertion percentage = 1.03% number of deletions = 2,835,111 mapped reads with deletion percentage = 1.29% homopolymer indels = 50.2% >>>>>>> Coverage mean coverageData = 6.5265X std coverageData = 831.1217X There is a 37.1% of reference with a coverageData >= 1X There is a 28.94% of reference with a coverageData >= 2X There is a 22.11% of reference with a coverageData >= 3X There is a 18.59% of reference with a coverageData >= 4X There is a 15.9% of reference with a coverageData >= 5X There is a 13.98% of reference with a coverageData >= 6X There is a 12.44% of reference with a coverageData >= 7X There is a 11.22% of reference with a coverageData >= 8X There is a 10.2% of reference with a coverageData >= 9X There is a 9.35% of reference with a coverageData >= 10X There is a 8.62% of reference with a coverageData >= 11X There is a 8% of reference with a coverageData >= 12X There is a 7.45% of reference with a coverageData >= 13X There is a 6.97% of reference with a coverageData >= 14X There is a 6.55% of reference with a coverageData >= 15X There is a 6.17% of reference with a coverageData >= 16X There is a 5.82% of reference with a coverageData >= 17X There is a 5.51% of reference with a coverageData >= 18X There is a 5.23% of reference with a coverageData >= 19X There is a 4.98% of reference with a coverageData >= 20X There is a 4.75% of reference with a coverageData >= 21X There is a 4.53% of reference with a coverageData >= 22X There is a 4.33% of reference with a coverageData >= 23X There is a 4.15% of reference with a coverageData >= 24X There is a 3.98% of reference with a coverageData >= 25X There is a 3.82% of reference with a coverageData >= 26X There is a 3.68% of reference with a coverageData >= 27X There is a 3.54% of reference with a coverageData >= 28X There is a 3.41% of reference with a coverageData >= 29X There is a 3.29% of reference with a coverageData >= 30X There is a 3.18% of reference with a coverageData >= 31X There is a 3.07% of reference with a coverageData >= 32X There is a 2.97% of reference with a coverageData >= 33X There is a 2.87% of reference with a coverageData >= 34X There is a 2.78% of reference with a coverageData >= 35X There is a 2.7% of reference with a coverageData >= 36X There is a 2.62% of reference with a coverageData >= 37X There is a 2.54% of reference with a coverageData >= 38X There is a 2.47% of reference with a coverageData >= 39X There is a 2.4% of reference with a coverageData >= 40X There is a 2.33% of reference with a coverageData >= 41X There is a 2.27% of reference with a coverageData >= 42X There is a 2.2% of reference with a coverageData >= 43X There is a 2.15% of reference with a coverageData >= 44X There is a 2.09% of reference with a coverageData >= 45X There is a 2.04% of reference with a coverageData >= 46X There is a 1.99% of reference with a coverageData >= 47X There is a 1.94% of reference with a coverageData >= 48X There is a 1.89% of reference with a coverageData >= 49X There is a 1.84% of reference with a coverageData >= 50X There is a 1.8% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1318322200 5.289143091041687 57.72569775819292 chr2 243199373 5898905818 24.25543185096945 2961.9819486107076 chr3 198022430 1299118138 6.560459529761351 37.31432734487808 chr4 191154276 1220604552 6.385442049959688 43.0027249106134 chr5 180915260 1029924576 5.692856290840253 36.72146428243846 chr6 171115067 957304511 5.594507414125022 28.16673868215693 chr7 159138663 812584978 5.106144306365072 27.768831706519805 chr8 146364022 959222728 6.553678389625013 62.24248210857597 chr9 141213431 782973877 5.544613366132291 62.67962571458032 chr10 135534747 747166810 5.512732539353912 33.4194309208675 chr11 135006516 734842450 5.443014691231644 33.27138227139315 chr12 133851895 758203840 5.664498362163644 27.745697581172468 chr13 115169878 483824285 4.20096203453476 21.724260888850903 chr14 107349540 524838967 4.889065821800448 28.979429268825847 chr15 102531392 467782537 4.562334792060562 72.05734452278551 chr16 90354753 356387357 3.9443122267181674 24.799644149442763 chr17 81195210 298676015 3.678493041646176 16.711938714869394 chr18 78077248 511290402 6.548519768524629 36.730859958824226 chr19 59128983 215308389 3.6413342167579645 44.25797912383706 chr20 63025520 288310264 4.574500361123557 25.376404849391513 chr21 48129895 217998623 4.529380814148878 31.55263879369309 chr22 51304566 150992037 2.9430526125101615 28.16093783775995 chrMT 16571 5190 0.3131977551143564 1.5651233133902598 chrX 155270560 40818564 0.2628866927510276 10.689931263885871 chrY 59373566 128694568 2.167539810561488 19.008432907469267