BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013200.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,697,985 number of mapped reads = 1,272,816 (74.96%) number of supplementary alignments = 11,140 (0.66%) number of secondary alignments = 0 number of mapped bases = 82,797,747 bp number of sequenced bases = 82,758,363 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 93,462 duplication rate = 5.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2933 >>>>>>> ACTG content number of A's = 22,381,261 bp (27.04%) number of C's = 14,907,473 bp (18.01%) number of T's = 26,763,639 bp (32.34%) number of G's = 18,704,824 bp (22.6%) number of N's = 1,166 bp (0%) GC percentage = 40.61% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 643,911 number of insertions = 5,855 mapped reads with insertion percentage = 0.46% number of deletions = 23,177 mapped reads with deletion percentage = 1.8% homopolymer indels = 46.73% >>>>>>> Coverage mean coverageData = 0.0267X std coverageData = 0.3185X There is a 1.98% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% 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 8406455 0.03372691697325801 0.5344333107610796 chr2 243199373 5724699 0.02353911907494926 0.43386360546011504 chr3 198022430 3207611 0.016198220575315635 0.16315358697084142 chr4 191154276 5911359 0.030924544947139972 0.2302067710081667 chr5 180915260 4021373 0.02222793699105316 0.19631189777505875 chr6 171115067 2970697 0.017360814872018255 0.18888568500935618 chr7 159138663 3739526 0.02349853850412203 0.30782482868711564 chr8 146364022 3136663 0.021430560305318747 0.3091738536756426 chr9 141213431 3336830 0.023629692844160128 0.337658573016564 chr10 135534747 5271139 0.03889142169572206 0.3235987941056303 chr11 135006516 5393858 0.03995257532606797 0.3436672431971228 chr12 133851895 6548736 0.04892523934756396 0.28876430756765903 chr13 115169878 1155239 0.010030739113920047 0.13077812320483856 chr14 107349540 3748245 0.034916265127917644 0.2506367956562225 chr15 102531392 1389583 0.01355275660355806 0.15115676256412336 chr16 90354753 2152124 0.0238186031010455 0.21502943839365232 chr17 81195210 3205284 0.039476269597677006 0.2563835239777268 chr18 78077248 1440049 0.01844390058420092 0.6550505680174243 chr19 59128983 2271312 0.03841283723753544 0.38225818609892215 chr20 63025520 2337234 0.037083930445952686 0.25018665626661213 chr21 48129895 1401504 0.0291191992004138 0.22175840882898096 chr22 51304566 1252525 0.02441351906183165 0.200991692676838 chrMT 16571 13642 0.8232454287610886 1.3428417724786386 chrX 155270560 4567907 0.0294190154270069 0.25704687540554777 chrY 59373566 194153 0.0032700242394064724 0.07808356166927254