BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777288.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 290,242,088 number of mapped reads = 283,972,727 (97.84%) number of supplementary alignments = 14,336,980 (4.94%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 142,432,378 number of mapped paired reads (second in pair) = 141,540,349 number of mapped paired reads (both in pair) = 282,481,026 number of mapped paired reads (singletons) = 1,491,701 number of mapped bases = 27,320,554,023 bp number of sequenced bases = 27,312,175,587 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,025,722 duplication rate = 22.9% >>>>>>> Insert size mean insert size = 159,733.8241 std insert size = 3,819,657.2113 median insert size = 154 >>>>>>> Mapping quality mean mapping quality = 52.9735 >>>>>>> ACTG content number of A's = 7,987,802,361 bp (29.25%) number of C's = 5,694,177,331 bp (20.85%) number of T's = 7,821,785,284 bp (28.64%) number of G's = 5,807,311,367 bp (21.26%) number of N's = 1,099,244 bp (0%) GC percentage = 42.11% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 141,369,758 number of insertions = 6,146,738 mapped reads with insertion percentage = 2.12% number of deletions = 3,370,447 mapped reads with deletion percentage = 1.15% homopolymer indels = 46.46% >>>>>>> Coverage mean coverageData = 8.8253X std coverageData = 84.3095X There is a 63.92% of reference with a coverageData >= 1X There is a 56.17% of reference with a coverageData >= 2X There is a 49.43% of reference with a coverageData >= 3X There is a 44.37% of reference with a coverageData >= 4X There is a 40.04% of reference with a coverageData >= 5X There is a 36.37% of reference with a coverageData >= 6X There is a 33.19% of reference with a coverageData >= 7X There is a 30.41% of reference with a coverageData >= 8X There is a 27.96% of reference with a coverageData >= 9X There is a 25.8% of reference with a coverageData >= 10X There is a 23.86% of reference with a coverageData >= 11X There is a 22.13% of reference with a coverageData >= 12X There is a 20.58% of reference with a coverageData >= 13X There is a 19.18% of reference with a coverageData >= 14X There is a 17.91% of reference with a coverageData >= 15X There is a 16.76% of reference with a coverageData >= 16X There is a 15.71% of reference with a coverageData >= 17X There is a 14.75% of reference with a coverageData >= 18X There is a 13.87% of reference with a coverageData >= 19X There is a 13.06% of reference with a coverageData >= 20X There is a 12.31% of reference with a coverageData >= 21X There is a 11.62% of reference with a coverageData >= 22X There is a 10.99% of reference with a coverageData >= 23X There is a 10.39% of reference with a coverageData >= 24X There is a 9.84% of reference with a coverageData >= 25X There is a 9.32% of reference with a coverageData >= 26X There is a 8.84% of reference with a coverageData >= 27X There is a 8.39% of reference with a coverageData >= 28X There is a 7.97% of reference with a coverageData >= 29X There is a 7.57% of reference with a coverageData >= 30X There is a 7.2% of reference with a coverageData >= 31X There is a 6.85% of reference with a coverageData >= 32X There is a 6.52% of reference with a coverageData >= 33X There is a 6.2% of reference with a coverageData >= 34X There is a 5.91% of reference with a coverageData >= 35X There is a 5.63% of reference with a coverageData >= 36X There is a 5.37% of reference with a coverageData >= 37X There is a 5.12% of reference with a coverageData >= 38X There is a 4.88% of reference with a coverageData >= 39X There is a 4.66% of reference with a coverageData >= 40X There is a 4.45% of reference with a coverageData >= 41X There is a 4.25% of reference with a coverageData >= 42X There is a 4.06% of reference with a coverageData >= 43X There is a 3.88% of reference with a coverageData >= 44X There is a 3.7% of reference with a coverageData >= 45X There is a 3.54% of reference with a coverageData >= 46X There is a 3.38% of reference with a coverageData >= 47X There is a 3.24% of reference with a coverageData >= 48X There is a 3.09% of reference with a coverageData >= 49X There is a 2.96% of reference with a coverageData >= 50X There is a 2.83% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2270355398 9.108725141350801 197.03047148355606 chr2 243199373 2368799961 9.74015652992658 61.35123424988123 chr3 198022430 1853886066 9.362000385511884 24.449880154856444 chr4 191154276 1798269866 9.407426836739974 64.05958938877357 chr5 180915260 1674239453 9.254274365799768 17.579765448152294 chr6 171115067 1583272153 9.252675294806155 46.543502437245266 chr7 159138663 1456851480 9.154604245983894 72.7058262171474 chr8 146364022 1380036319 9.428794727983083 35.36907398716611 chr9 141213431 1183352458 8.379886032228761 84.96853717881467 chr10 135534747 1441350204 10.634543804475468 177.25083648647046 chr11 135006516 1298651328 9.61917518114459 45.99440552441287 chr12 133851895 1230266007 9.191248334586522 17.00404973303856 chr13 115169878 858931926 7.45795637640599 14.65757713571839 chr14 107349540 845342047 7.874668554704566 16.926136285092987 chr15 102531392 779969467 7.6071284295057655 15.112645978894651 chr16 90354753 806017494 8.920587652981576 33.33202282487306 chr17 81195210 770393379 9.488162897786705 48.971332495095034 chr18 78077248 768265021 9.839806610499387 112.80769700197064 chr19 59128983 523343047 8.850871779749705 111.74622730851436 chr20 63025520 610578094 9.687791453366827 23.588723590655487 chr21 48129895 373900840 7.768577928541086 34.238102049819084 chr22 51304566 332233852 6.4757170346202715 15.188979733031733 chrMT 16571 121392127 7325.576428700742 1428.4628958208718 chrX 155270560 757425286 4.878099789168018 22.646996373664063 chrY 59373566 233430750 3.931560216544851 63.813922542884775