BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1954923.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 = 17,552,184 number of mapped reads = 17,088,532 (97.36%) number of supplementary alignments = 41,543 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,712,026 number of mapped paired reads (second in pair) = 8,376,506 number of mapped paired reads (both in pair) = 16,727,682 number of mapped paired reads (singletons) = 360,850 number of mapped bases = 1,599,752,447 bp number of sequenced bases = 1,598,704,015 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 751,289 duplication rate = 3.71% >>>>>>> Insert size mean insert size = 28,870.4277 std insert size = 1,721,580.6674 median insert size = 329 >>>>>>> Mapping quality mean mapping quality = 54.2441 >>>>>>> ACTG content number of A's = 460,337,435 bp (28.79%) number of C's = 315,606,539 bp (19.74%) number of T's = 459,864,305 bp (28.76%) number of G's = 362,794,697 bp (22.69%) number of N's = 101,039 bp (0.01%) GC percentage = 42.43% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 14,191,460 number of insertions = 261,569 mapped reads with insertion percentage = 1.51% number of deletions = 763,517 mapped reads with deletion percentage = 4.36% homopolymer indels = 54.29% >>>>>>> Coverage mean coverageData = 0.5168X std coverageData = 1.4493X There is a 25.92% of reference with a coverageData >= 1X There is a 11.47% of reference with a coverageData >= 2X There is a 5.8% of reference with a coverageData >= 3X There is a 3.18% of reference with a coverageData >= 4X There is a 1.84% of reference with a coverageData >= 5X There is a 1.11% of reference with a coverageData >= 6X There is a 0.69% of reference with a coverageData >= 7X There is a 0.44% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 134713399 0.5404736744868531 1.611654682063505 chr2 243199373 140592169 0.5780942905638166 2.2377748655059273 chr3 198022430 109917472 0.5550758669106323 1.2503937556878963 chr4 191154276 91897658 0.4807512545521085 1.2571101260324964 chr5 180915260 99675129 0.5509492621020471 1.2374687709272445 chr6 171115067 90452868 0.5286084363336632 1.2318421794978807 chr7 159138663 83066097 0.5219730732562458 1.2479217284185644 chr8 146364022 82546390 0.5639800606189955 1.3372511377517406 chr9 141213431 69353409 0.49112473586170424 1.680634689386865 chr10 135534747 78030827 0.575725625547521 1.4161586527751104 chr11 135006516 77514215 0.5741516579836784 1.4449507972827171 chr12 133851895 72168291 0.5391652542535913 1.2499191481346024 chr13 115169878 47830263 0.4153018465470633 1.0765959632763724 chr14 107349540 72216302 0.6727211127313634 1.5566519933074534 chr15 102531392 49878231 0.48646790048456573 1.2165435661958923 chr16 90354753 49916256 0.5524474844173388 1.5615360233697224 chr17 81195210 43667667 0.5378108757893477 1.3345302855182342 chr18 78077248 43298532 0.5545601709732392 1.9258857822321276 chr19 59128983 25318214 0.42818619085669035 1.2809446190283482 chr20 63025520 40598388 0.6441579220607779 1.4496787698652929 chr21 48129895 20534409 0.42664562222710023 1.6288404372362622 chr22 51304566 21483831 0.41875085737982853 1.1723706461379428 chrMT 16571 196935 11.884315973688974 7.718469357129316 chrX 155270560 46118583 0.2970207810160535 0.8473310326039498 chrY 59373566 8766912 0.14765682088220877 0.918488643354557