BamQC report ----------------------------------- >>>>>>> Input bam file = SRR630578.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 30,916,924 number of mapped reads = 30,439,069 (98.45%) number of supplementary alignments = 65,512 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,272,321 number of mapped paired reads (second in pair) = 15,166,748 number of mapped paired reads (both in pair) = 30,269,568 number of mapped paired reads (singletons) = 169,501 number of mapped bases = 2,958,886,289 bp number of sequenced bases = 2,956,639,113 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,574,066 duplication rate = 9.51% >>>>>>> Insert size mean insert size = 27,952.1562 std insert size = 1,640,670.9012 median insert size = 198 >>>>>>> Mapping quality mean mapping quality = 54.0341 >>>>>>> ACTG content number of A's = 878,745,785 bp (29.72%) number of C's = 576,124,349 bp (19.49%) number of T's = 886,855,506 bp (30%) number of G's = 614,467,113 bp (20.78%) number of N's = 446,360 bp (0.02%) GC percentage = 40.27% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 26,699,069 number of insertions = 556,911 mapped reads with insertion percentage = 1.8% number of deletions = 1,672,965 mapped reads with deletion percentage = 5.34% homopolymer indels = 54.58% >>>>>>> Coverage mean coverageData = 0.9558X std coverageData = 4.8058X There is a 17.53% of reference with a coverageData >= 1X There is a 12.05% of reference with a coverageData >= 2X There is a 8.94% of reference with a coverageData >= 3X There is a 7.05% of reference with a coverageData >= 4X There is a 5.73% of reference with a coverageData >= 5X There is a 4.77% of reference with a coverageData >= 6X There is a 4.04% of reference with a coverageData >= 7X There is a 3.46% of reference with a coverageData >= 8X There is a 3% of reference with a coverageData >= 9X There is a 2.62% of reference with a coverageData >= 10X There is a 2.3% of reference with a coverageData >= 11X There is a 2.04% of reference with a coverageData >= 12X There is a 1.81% of reference with a coverageData >= 13X There is a 1.62% of reference with a coverageData >= 14X There is a 1.45% of reference with a coverageData >= 15X There is a 1.3% of reference with a coverageData >= 16X There is a 1.18% of reference with a coverageData >= 17X There is a 1.06% of reference with a coverageData >= 18X There is a 0.97% of reference with a coverageData >= 19X There is a 0.88% of reference with a coverageData >= 20X There is a 0.8% of reference with a coverageData >= 21X There is a 0.73% of reference with a coverageData >= 22X There is a 0.67% of reference with a coverageData >= 23X There is a 0.61% of reference with a coverageData >= 24X There is a 0.56% of reference with a coverageData >= 25X There is a 0.52% of reference with a coverageData >= 26X There is a 0.48% of reference with a coverageData >= 27X There is a 0.44% of reference with a coverageData >= 28X There is a 0.4% of reference with a coverageData >= 29X There is a 0.37% of reference with a coverageData >= 30X There is a 0.35% of reference with a coverageData >= 31X There is a 0.32% of reference with a coverageData >= 32X There is a 0.3% of reference with a coverageData >= 33X There is a 0.28% of reference with a coverageData >= 34X There is a 0.26% of reference with a coverageData >= 35X There is a 0.24% of reference with a coverageData >= 36X There is a 0.22% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.13% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.11% of reference with a coverageData >= 47X There is a 0.11% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.09% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 235096867 0.9432147693626007 6.108570465231565 chr2 243199373 261369490 1.0747128447572107 5.721878157678609 chr3 198022430 209008528 1.0554790586096736 4.113164718874056 chr4 191154276 188769036 0.9875219113591788 4.888548348144047 chr5 180915260 182562950 1.0091075235997229 4.0639167309694555 chr6 171115067 177110620 1.035038136063144 4.298169425749168 chr7 159138663 157133397 0.9873992531909106 4.10484632142872 chr8 146364022 152826749 1.0441551613005005 4.216376662929863 chr9 141213431 126976664 0.8991826280320319 6.771092848143467 chr10 135534747 135260836 0.9979790348522213 4.509037997320176 chr11 135006516 141749723 1.049947270693216 5.142929547417569 chr12 133851895 133371825 0.996413423956381 4.137444969743579 chr13 115169878 92629097 0.8042823228483406 3.5142204278434304 chr14 107349540 91596283 0.853252682778147 3.8497251562528505 chr15 102531392 86504375 0.8436867315719268 3.7270627191785084 chr16 90354753 85384061 0.9449869338915685 5.13562823097105 chr17 81195210 70799919 0.871971622463936 3.8957168444234322 chr18 78077248 80304689 1.028528682260932 7.571130913801939 chr19 59128983 41041115 0.6940947217035679 3.9806891904289246 chr20 63025520 62991798 0.9994649468977012 4.229620992425492 chr21 48129895 39725475 0.8253804626002197 4.5507421776316 chr22 51304566 29263907 0.5703957616559898 2.9948181474046383 chrMT 16571 4805 0.28996439563092147 0.835760852778694 chrX 155270560 172130578 1.1085847697077926 4.562650231415305 chrY 59373566 5273502 0.0888190209090692 2.693208209586357