BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695946.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 153,320,160 number of mapped reads = 152,242,275 (99.3%) number of supplementary alignments = 2,059,325 (1.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 76,310,972 number of mapped paired reads (second in pair) = 75,931,303 number of mapped paired reads (both in pair) = 151,550,384 number of mapped paired reads (singletons) = 691,891 number of mapped bases = 15,102,254,752 bp number of sequenced bases = 15,098,040,841 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,574,288 duplication rate = 9.29% >>>>>>> Insert size mean insert size = 76,402.0082 std insert size = 2,710,302.3987 median insert size = 338 >>>>>>> Mapping quality mean mapping quality = 54.061 >>>>>>> ACTG content number of A's = 4,263,423,336 bp (28.24%) number of C's = 3,247,333,219 bp (21.51%) number of T's = 4,240,460,815 bp (28.09%) number of G's = 3,346,567,091 bp (22.17%) number of N's = 256,380 bp (0%) GC percentage = 43.67% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 55,749,022 number of insertions = 2,005,306 mapped reads with insertion percentage = 1.28% number of deletions = 1,742,641 mapped reads with deletion percentage = 1.11% homopolymer indels = 44.61% >>>>>>> Coverage mean coverageData = 4.8785X std coverageData = 11.701X There is a 71.58% of reference with a coverageData >= 1X There is a 57.62% of reference with a coverageData >= 2X There is a 46.99% of reference with a coverageData >= 3X There is a 38.76% of reference with a coverageData >= 4X There is a 32.27% of reference with a coverageData >= 5X There is a 27.12% of reference with a coverageData >= 6X There is a 22.98% of reference with a coverageData >= 7X There is a 19.62% of reference with a coverageData >= 8X There is a 16.86% of reference with a coverageData >= 9X There is a 14.59% of reference with a coverageData >= 10X There is a 12.7% of reference with a coverageData >= 11X There is a 11.11% of reference with a coverageData >= 12X There is a 9.77% of reference with a coverageData >= 13X There is a 8.63% of reference with a coverageData >= 14X There is a 7.66% of reference with a coverageData >= 15X There is a 6.82% of reference with a coverageData >= 16X There is a 6.1% of reference with a coverageData >= 17X There is a 5.47% of reference with a coverageData >= 18X There is a 4.93% of reference with a coverageData >= 19X There is a 4.45% of reference with a coverageData >= 20X There is a 4.03% of reference with a coverageData >= 21X There is a 3.66% of reference with a coverageData >= 22X There is a 3.33% of reference with a coverageData >= 23X There is a 3.04% of reference with a coverageData >= 24X There is a 2.78% of reference with a coverageData >= 25X There is a 2.55% of reference with a coverageData >= 26X There is a 2.34% of reference with a coverageData >= 27X There is a 2.16% of reference with a coverageData >= 28X There is a 1.99% of reference with a coverageData >= 29X There is a 1.84% of reference with a coverageData >= 30X There is a 1.7% of reference with a coverageData >= 31X There is a 1.58% of reference with a coverageData >= 32X There is a 1.46% of reference with a coverageData >= 33X There is a 1.36% of reference with a coverageData >= 34X There is a 1.27% of reference with a coverageData >= 35X There is a 1.18% of reference with a coverageData >= 36X There is a 1.1% of reference with a coverageData >= 37X There is a 1.03% of reference with a coverageData >= 38X There is a 0.96% of reference with a coverageData >= 39X There is a 0.9% of reference with a coverageData >= 40X There is a 0.85% of reference with a coverageData >= 41X There is a 0.79% of reference with a coverageData >= 42X There is a 0.75% of reference with a coverageData >= 43X There is a 0.7% of reference with a coverageData >= 44X There is a 0.66% of reference with a coverageData >= 45X There is a 0.62% of reference with a coverageData >= 46X There is a 0.59% of reference with a coverageData >= 47X There is a 0.56% of reference with a coverageData >= 48X There is a 0.53% of reference with a coverageData >= 49X There is a 0.5% of reference with a coverageData >= 50X There is a 0.47% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1907052451 7.651144231251484 16.736086340741597 chr2 243199373 1172866730 4.822655237684351 16.548959689096367 chr3 198022430 959168801 4.843738161378991 7.346738101947641 chr4 191154276 781424517 4.087925906507056 7.464207883010985 chr5 180915260 849814656 4.697307767183377 7.4251785394165415 chr6 171115067 559917840 3.2721714681033904 7.244847925206818 chr7 159138663 1090884811 6.854932613075931 10.242525132878033 chr8 146364022 519629821 3.550256503609883 6.979918083103423 chr9 141213431 467249286 3.308816184772113 12.744403706360659 chr10 135534747 756040713 5.578205808728886 15.647960958079043 chr11 135006516 878750974 6.508952308642644 10.79305638579476 chr12 133851895 734814684 5.489759289549094 9.249055922130752 chr13 115169878 291935759 2.53482737039975 6.2007993358064075 chr14 107349540 492885788 4.591410340463499 9.60187248945423 chr15 102531392 336374321 3.280695935543331 6.464246904370388 chr16 90354753 528620859 5.8505041677220895 15.401329271676087 chr17 81195210 570519234 7.026513435952688 13.617306815260235 chr18 78077248 483526143 6.192919901582597 17.222007150128707 chr19 59128983 484630701 8.196161618406324 15.81710883390005 chr20 63025520 407118337 6.45957918316263 10.600318179687406 chr21 48129895 184667023 3.8368465794492175 9.009231420296578 chr22 51304566 355267697 6.924679900810388 15.253260729778411 chrMT 16571 2424505 146.31012008931265 49.692219990127505 chrX 155270560 224915827 1.4485413525912445 4.63274872123129 chrY 59373566 61753274 1.0400802606331578 13.52714540600355