BamQC report ----------------------------------- >>>>>>> Input bam file = SRR090129.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 20,912,753 number of mapped reads = 16,810,627 (80.38%) number of supplementary alignments = 762 (0%) number of secondary alignments = 0 number of mapped bases = 793,273,880 bp number of sequenced bases = 793,126,063 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,000,970 duplication rate = 11.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3467 >>>>>>> ACTG content number of A's = 233,958,772 bp (29.5%) number of C's = 160,789,367 bp (20.27%) number of T's = 230,504,365 bp (29.06%) number of G's = 167,708,495 bp (21.15%) number of N's = 165,064 bp (0.02%) GC percentage = 41.42% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 4,882,801 number of insertions = 31,028 mapped reads with insertion percentage = 0.18% number of deletions = 96,933 mapped reads with deletion percentage = 0.58% homopolymer indels = 45.92% >>>>>>> Coverage mean coverageData = 0.2563X std coverageData = 1.3816X There is a 12.25% of reference with a coverageData >= 1X There is a 5.63% of reference with a coverageData >= 2X There is a 3% of reference with a coverageData >= 3X There is a 1.71% of reference with a coverageData >= 4X There is a 1.01% of reference with a coverageData >= 5X There is a 0.62% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.25% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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% 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 65061359 0.2610278712204292 2.169090815189295 chr2 243199373 82245957 0.33818326085898254 1.5540971769502296 chr3 198022430 73036660 0.36883023806949544 1.1473286808027887 chr4 191154276 41243600 0.21576080254673455 0.8608045289394594 chr5 180915260 36502285 0.201764544350764 0.8169135157547222 chr6 171115067 43184200 0.25236936032056134 0.9784978326342025 chr7 159138663 56886772 0.35746669556976235 2.1728707559592952 chr8 146364022 68924540 0.47091176546105024 2.4911221962077272 chr9 141213431 25725349 0.18217352852222676 1.2173946287232724 chr10 135534747 24152668 0.17820277482054103 1.0908751134388337 chr11 135006516 33855285 0.25076778516379167 1.1315319617909734 chr12 133851895 27820539 0.20784568645815585 0.8500946460039766 chr13 115169878 23879335 0.20734010849607742 0.8210117419721641 chr14 107349540 28332799 0.26393032517885034 0.9611931793940863 chr15 102531392 21621503 0.21087690880077 0.8335024675536923 chr16 90354753 16495128 0.1825596048057372 0.8169896388377949 chr17 81195210 16204426 0.19957366943197757 0.9345271105134051 chr18 78077248 30102973 0.3855537147006001 1.9831718529027775 chr19 59128983 13530438 0.2288292020852109 1.4746789387702206 chr20 63025520 19700084 0.31257312910706647 1.0931859201444583 chr21 48129895 11528466 0.23952817682232633 1.0191055513111194 chr22 51304566 6341948 0.12361371500540518 0.632160877833056 chrMT 16571 52584 3.173254480719329 3.2877869074909083 chrX 155270560 24836726 0.15995772798140226 0.7985264317650301 chrY 59373566 2008256 0.03382407585220669 1.1526120639201578