BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505980.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 8,222,788 number of mapped reads = 5,330,930 (64.83%) number of supplementary alignments = 290 (0%) number of secondary alignments = 0 number of mapped bases = 244,394,866 bp number of sequenced bases = 244,351,334 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 540,556 duplication rate = 7.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4437 >>>>>>> ACTG content number of A's = 71,471,390 bp (29.25%) number of C's = 51,406,173 bp (21.04%) number of T's = 69,631,916 bp (28.5%) number of G's = 51,840,780 bp (21.22%) number of N's = 1,075 bp (0%) GC percentage = 42.25% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 1,215,334 number of insertions = 10,850 mapped reads with insertion percentage = 0.2% number of deletions = 31,758 mapped reads with deletion percentage = 0.59% homopolymer indels = 42.98% >>>>>>> Coverage mean coverageData = 0.0789X std coverageData = 0.7188X There is a 5.01% of reference with a coverageData >= 1X There is a 1.64% of reference with a coverageData >= 2X There is a 0.63% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 19450851 0.07803732212165682 1.4488971961979347 chr2 243199373 20484446 0.08422902471874383 0.6132158057415541 chr3 198022430 16329052 0.08246061822390524 0.4235828389598651 chr4 191154276 15740313 0.08234350457323801 0.4507861785359787 chr5 180915260 14807840 0.0818495907973711 0.4263000072332336 chr6 171115067 14252272 0.08329057312060077 0.5141893452286396 chr7 159138663 13913544 0.0874303185518154 1.074488896718489 chr8 146364022 12571968 0.0858952072251745 0.9922340646637108 chr9 141213431 10174943 0.07205364906118597 0.5406400602024735 chr10 135534747 11820494 0.08721375338532192 0.733762582752749 chr11 135006516 11227537 0.08316292674347658 0.6389989927883528 chr12 133851895 10825582 0.08087731593191116 0.44383145952137604 chr13 115169878 7733991 0.06715289739214624 0.3769062456748901 chr14 107349540 7381617 0.0687624464902225 0.5383409148862445 chr15 102531392 6967192 0.06795179372967061 0.38249093415046925 chr16 90354753 6870420 0.07603827991207059 0.4455010145984737 chr17 81195210 6314695 0.07777176757101804 0.4684187648639534 chr18 78077248 6532465 0.08366669122354313 1.0110217468315568 chr19 59128983 4753543 0.08039277455524645 0.9771514800238043 chr20 63025520 5094220 0.08082789320897313 0.4451420155223386 chr21 48129895 3243208 0.06738448110057169 0.4412000788925995 chr22 51304566 2781776 0.054220827050754115 0.3457543781892087 chrMT 16571 89070 5.375052803089735 4.825771062595795 chrX 155270560 14211337 0.09152628160805241 0.5123807820144952 chrY 59373566 822490 0.01385279772483263 0.26796321383633365