BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504594.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 = 365,590,394 number of mapped reads = 349,912,673 (95.71%) number of supplementary alignments = 1,011,548 (0.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 175,162,923 number of mapped paired reads (second in pair) = 174,749,750 number of mapped paired reads (both in pair) = 347,098,772 number of mapped paired reads (singletons) = 2,813,901 number of mapped bases = 33,623,800,123 bp number of sequenced bases = 33,613,001,831 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,056,110 duplication rate = 18.05% >>>>>>> Insert size mean insert size = 33,970.9612 std insert size = 1,747,548.5808 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 53.3737 >>>>>>> ACTG content number of A's = 9,549,933,489 bp (28.41%) number of C's = 7,210,339,592 bp (21.45%) number of T's = 9,454,979,467 bp (28.13%) number of G's = 7,387,499,526 bp (21.98%) number of N's = 10,249,757 bp (0.03%) GC percentage = 43.43% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 186,362,042 number of insertions = 3,394,592 mapped reads with insertion percentage = 0.93% number of deletions = 4,175,293 mapped reads with deletion percentage = 1.15% homopolymer indels = 40.38% >>>>>>> Coverage mean coverageData = 10.8615X std coverageData = 95.7155X There is a 90.88% of reference with a coverageData >= 1X There is a 89.14% of reference with a coverageData >= 2X There is a 86.18% of reference with a coverageData >= 3X There is a 82.05% of reference with a coverageData >= 4X There is a 76.88% of reference with a coverageData >= 5X There is a 70.96% of reference with a coverageData >= 6X There is a 64.59% of reference with a coverageData >= 7X There is a 58.05% of reference with a coverageData >= 8X There is a 51.6% of reference with a coverageData >= 9X There is a 45.42% of reference with a coverageData >= 10X There is a 39.64% of reference with a coverageData >= 11X There is a 34.36% of reference with a coverageData >= 12X There is a 29.62% of reference with a coverageData >= 13X There is a 25.42% of reference with a coverageData >= 14X There is a 21.75% of reference with a coverageData >= 15X There is a 18.58% of reference with a coverageData >= 16X There is a 15.85% of reference with a coverageData >= 17X There is a 13.54% of reference with a coverageData >= 18X There is a 11.57% of reference with a coverageData >= 19X There is a 9.92% of reference with a coverageData >= 20X There is a 8.53% of reference with a coverageData >= 21X There is a 7.36% of reference with a coverageData >= 22X There is a 6.39% of reference with a coverageData >= 23X There is a 5.57% of reference with a coverageData >= 24X There is a 4.89% of reference with a coverageData >= 25X There is a 4.31% of reference with a coverageData >= 26X There is a 3.83% of reference with a coverageData >= 27X There is a 3.42% of reference with a coverageData >= 28X There is a 3.08% of reference with a coverageData >= 29X There is a 2.78% of reference with a coverageData >= 30X There is a 2.53% of reference with a coverageData >= 31X There is a 2.32% of reference with a coverageData >= 32X There is a 2.13% of reference with a coverageData >= 33X There is a 1.97% of reference with a coverageData >= 34X There is a 1.83% of reference with a coverageData >= 35X There is a 1.71% of reference with a coverageData >= 36X There is a 1.6% of reference with a coverageData >= 37X There is a 1.5% of reference with a coverageData >= 38X There is a 1.41% of reference with a coverageData >= 39X There is a 1.33% of reference with a coverageData >= 40X There is a 1.26% of reference with a coverageData >= 41X There is a 1.2% of reference with a coverageData >= 42X There is a 1.14% of reference with a coverageData >= 43X There is a 1.09% of reference with a coverageData >= 44X There is a 1.04% of reference with a coverageData >= 45X There is a 0.99% of reference with a coverageData >= 46X There is a 0.95% of reference with a coverageData >= 47X There is a 0.91% of reference with a coverageData >= 48X There is a 0.87% of reference with a coverageData >= 49X There is a 0.84% of reference with a coverageData >= 50X There is a 0.81% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3127165353 12.546269054230361 173.4208961016225 chr2 243199373 2374796169 9.764812054017918 57.63690026758582 chr3 198022430 1990032383 10.049530161810457 16.554380056231967 chr4 191154276 1905118866 9.96639419146449 115.06968877932982 chr5 180915260 1586703001 8.770421030265773 10.402649065192994 chr6 171115067 1575819766 9.209123390636314 22.655462953274064 chr7 159138663 2836619043 17.824826409406242 138.28039188664374 chr8 146364022 2955934421 20.19577202517706 67.02198965358063 chr9 141213431 1212058986 8.583170718371683 60.729226048318345 chr10 135534747 1636715833 12.075986927544122 259.2411111906216 chr11 135006516 1443232512 10.690095224737153 39.00180401645587 chr12 133851895 1257473052 9.394510641780604 8.830749163646397 chr13 115169878 815577784 7.081519909224876 6.482518512011074 chr14 107349540 1091129750 10.164270382527954 9.571911399775338 chr15 102531392 878336477 8.566512751528819 7.30974010719612 chr16 90354753 933780674 10.334604910048284 73.48161480062078 chr17 81195210 1042845693 12.843684904565183 45.14924411828945 chr18 78077248 573480270 7.345036930604931 95.00286887426113 chr19 59128983 672685931 11.376585506299001 90.1693431237477 chr20 63025520 1413742994 22.43127853605968 29.106571064481948 chr21 48129895 403442037 8.382358552828757 40.586506977100235 chr22 51304566 454033065 8.849759395684197 9.496317084757173 chrMT 16571 120263461 7257.465512039104 1548.8584089641595 chrX 155270560 1193551485 7.686914280466303 18.817288916159804 chrY 59373566 129261117 2.177081918913208 117.13602908315526