BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505916.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 = 7,015,067 number of mapped reads = 4,953,289 (70.61%) number of supplementary alignments = 266 (0%) number of secondary alignments = 0 number of mapped bases = 228,057,326 bp number of sequenced bases = 228,010,108 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 236,799 duplication rate = 3.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5927 >>>>>>> ACTG content number of A's = 67,664,462 bp (29.68%) number of C's = 46,360,770 bp (20.33%) number of T's = 66,869,326 bp (29.33%) number of G's = 47,114,849 bp (20.66%) number of N's = 701 bp (0%) GC percentage = 41% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,148,396 number of insertions = 10,352 mapped reads with insertion percentage = 0.21% number of deletions = 34,004 mapped reads with deletion percentage = 0.68% homopolymer indels = 45.97% >>>>>>> Coverage mean coverageData = 0.0737X std coverageData = 0.5972X There is a 5.93% of reference with a coverageData >= 1X There is a 1.02% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 24542327 0.09846445678464327 1.276893834280485 chr2 243199373 15120489 0.06217322361271055 0.42015294611174203 chr3 198022430 15032319 0.0759122034811915 0.33013043663708974 chr4 191154276 10510862 0.05498627715761901 0.28247281135982344 chr5 180915260 13642485 0.07540814964973104 0.332984493257744 chr6 171115067 17001681 0.09935817633171952 0.4714062995999343 chr7 159138663 15744785 0.09893752217837849 0.9349423333693911 chr8 146364022 14871791 0.10160824222225869 0.81812774148094 chr9 141213431 6324809 0.04478900452464752 0.3665839536900681 chr10 135534747 7315260 0.05397331800088136 0.6289231542487884 chr11 135006516 11922218 0.08830846357075091 0.5395146596984407 chr12 133851895 7266949 0.05429096838711174 0.2963124049283688 chr13 115169878 5581437 0.04846264576228864 0.25821155930281275 chr14 107349540 8573170 0.07986219596283319 0.5827946332499199 chr15 102531392 4440554 0.04330921402100929 0.2445755947392143 chr16 90354753 7550252 0.08356231132633388 0.4033811399536941 chr17 81195210 3818535 0.04702906735508166 0.3011579911739246 chr18 78077248 5655968 0.07244066799075705 0.6564199438033006 chr19 59128983 5558934 0.0940136920670528 0.8544791614533634 chr20 63025520 5785261 0.09179235649305234 0.3654896131497717 chr21 48129895 3417958 0.07101528062756006 0.3388211946203859 chr22 51304566 1698146 0.03309931517596309 0.21386613102564475 chrMT 16571 13163 0.7943395087803995 1.1489274043355437 chrX 155270560 15989516 0.10297841393758096 0.4435837475701361 chrY 59373566 678457 0.011426920188691379 0.15206156080597458