BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438272.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 739,091,198 number of mapped reads = 736,831,887 (99.69%) number of supplementary alignments = 12,453,145 (1.68%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 368,577,977 number of mapped paired reads (second in pair) = 368,253,910 number of mapped paired reads (both in pair) = 735,284,662 number of mapped paired reads (singletons) = 1,547,225 number of mapped bases = 106,221,433,311 bp number of sequenced bases = 106,192,703,599 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 302,903,615 duplication rate = 38.28% >>>>>>> Insert size mean insert size = 40,447.7013 std insert size = 1,959,376.6995 median insert size = 243 >>>>>>> Mapping quality mean mapping quality = 55.1259 >>>>>>> ACTG content number of A's = 32,114,259,968 bp (30.24%) number of C's = 21,232,512,428 bp (19.99%) number of T's = 30,645,600,541 bp (28.86%) number of G's = 22,199,679,463 bp (20.91%) number of N's = 651,199 bp (0%) GC percentage = 40.9% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 539,852,840 number of insertions = 13,146,844 mapped reads with insertion percentage = 1.75% number of deletions = 11,658,552 mapped reads with deletion percentage = 1.56% homopolymer indels = 48.37% >>>>>>> Coverage mean coverageData = 34.3126X std coverageData = 75.5434X There is a 91.6% of reference with a coverageData >= 1X There is a 91% of reference with a coverageData >= 2X There is a 90.32% of reference with a coverageData >= 3X There is a 89.57% of reference with a coverageData >= 4X There is a 88.71% of reference with a coverageData >= 5X There is a 87.77% of reference with a coverageData >= 6X There is a 86.73% of reference with a coverageData >= 7X There is a 85.59% of reference with a coverageData >= 8X There is a 84.36% of reference with a coverageData >= 9X There is a 83.04% of reference with a coverageData >= 10X There is a 81.63% of reference with a coverageData >= 11X There is a 80.15% of reference with a coverageData >= 12X There is a 78.59% of reference with a coverageData >= 13X There is a 76.97% of reference with a coverageData >= 14X There is a 75.3% of reference with a coverageData >= 15X There is a 73.58% of reference with a coverageData >= 16X There is a 71.82% of reference with a coverageData >= 17X There is a 70.03% of reference with a coverageData >= 18X There is a 68.22% of reference with a coverageData >= 19X There is a 66.39% of reference with a coverageData >= 20X There is a 64.55% of reference with a coverageData >= 21X There is a 62.7% of reference with a coverageData >= 22X There is a 60.86% of reference with a coverageData >= 23X There is a 59.02% of reference with a coverageData >= 24X There is a 57.2% of reference with a coverageData >= 25X There is a 55.4% of reference with a coverageData >= 26X There is a 53.61% of reference with a coverageData >= 27X There is a 51.85% of reference with a coverageData >= 28X There is a 50.12% of reference with a coverageData >= 29X There is a 48.42% of reference with a coverageData >= 30X There is a 46.76% of reference with a coverageData >= 31X There is a 45.13% of reference with a coverageData >= 32X There is a 43.53% of reference with a coverageData >= 33X There is a 41.98% of reference with a coverageData >= 34X There is a 40.46% of reference with a coverageData >= 35X There is a 38.99% of reference with a coverageData >= 36X There is a 37.55% of reference with a coverageData >= 37X There is a 36.15% of reference with a coverageData >= 38X There is a 34.8% of reference with a coverageData >= 39X There is a 33.49% of reference with a coverageData >= 40X There is a 32.21% of reference with a coverageData >= 41X There is a 30.98% of reference with a coverageData >= 42X There is a 29.79% of reference with a coverageData >= 43X There is a 28.64% of reference with a coverageData >= 44X There is a 27.53% of reference with a coverageData >= 45X There is a 26.45% of reference with a coverageData >= 46X There is a 25.41% of reference with a coverageData >= 47X There is a 24.42% of reference with a coverageData >= 48X There is a 23.45% of reference with a coverageData >= 49X There is a 22.52% of reference with a coverageData >= 50X There is a 21.63% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8645050949 34.68417015097427 32.18521343064517 chr2 243199373 9417895698 38.72499991190356 117.88136890582143 chr3 198022430 7642443917 38.59382958284069 78.98522031151052 chr4 191154276 7155427730 37.43273694803458 27.432397239729173 chr5 180915260 6866311511 37.953191516293316 29.69628887806172 chr6 171115067 6521133880 38.109641624954044 29.226811998488245 chr7 159138663 5672249187 35.64343874750286 28.352984708604684 chr8 146364022 5545557845 37.888804702292205 28.530840641422795 chr9 141213431 4688137190 33.198946848051584 34.41907409406498 chr10 135534747 5143925069 37.95281418867444 37.5897123591696 chr11 135006516 5016560318 37.15791257067918 29.293454325373943 chr12 133851895 4976530359 37.17937918622669 27.874486537426794 chr13 115169878 3744144833 32.509757742384686 28.750134605794617 chr14 107349540 3356603864 31.26798553584859 30.041102015588077 chr15 102531392 3053383085 29.7799827490882 29.767808393061948 chr16 90354753 2863610097 31.692965803359563 52.510150111946935 chr17 81195210 2542289492 31.310830922168932 37.3610153124356 chr18 78077248 3001686651 38.445087754629874 29.944166110802136 chr19 59128983 1528860236 25.85635941007137 108.16541846825984 chr20 63025520 2328843109 36.95079563008762 31.89330239565775 chr21 48129895 1399449560 29.076513879783032 52.25987763466071 chr22 51304566 1116470998 21.761630300117925 28.775155090654415 chrMT 16571 374398644 22593.605938084605 8596.452364461336 chrX 155270560 3089505532 19.897561598283666 19.77481608047079 chrY 59373566 530963557 8.942760099671291 27.062124967097425