BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1954924.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 = 18,092,594 number of mapped reads = 17,644,813 (97.53%) number of supplementary alignments = 43,458 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,981,655 number of mapped paired reads (second in pair) = 8,663,158 number of mapped paired reads (both in pair) = 17,300,360 number of mapped paired reads (singletons) = 344,453 number of mapped bases = 1,652,401,920 bp number of sequenced bases = 1,651,319,567 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 796,175 duplication rate = 3.8% >>>>>>> Insert size mean insert size = 30,048.3606 std insert size = 1,734,453.5285 median insert size = 329 >>>>>>> Mapping quality mean mapping quality = 54.2588 >>>>>>> ACTG content number of A's = 475,938,062 bp (28.82%) number of C's = 325,565,805 bp (19.72%) number of T's = 475,472,549 bp (28.79%) number of G's = 374,295,083 bp (22.67%) number of N's = 48,068 bp (0%) GC percentage = 42.38% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 14,147,178 number of insertions = 269,991 mapped reads with insertion percentage = 1.51% number of deletions = 789,658 mapped reads with deletion percentage = 4.37% homopolymer indels = 54.35% >>>>>>> Coverage mean coverageData = 0.5338X std coverageData = 1.4901X There is a 26.39% of reference with a coverageData >= 1X There is a 11.84% of reference with a coverageData >= 2X There is a 6.06% of reference with a coverageData >= 3X There is a 3.36% of reference with a coverageData >= 4X There is a 1.97% of reference with a coverageData >= 5X There is a 1.2% of reference with a coverageData >= 6X There is a 0.75% of reference with a coverageData >= 7X There is a 0.48% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.21% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% 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 0.01% 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 138768544 0.5567430221166831 1.6464874524998407 chr2 243199373 145153117 0.5968482369401503 2.2927607061066975 chr3 198022430 113443091 0.5728800065729928 1.2833917876389267 chr4 191154276 95354439 0.4988349776700784 1.3023379560571975 chr5 180915260 103123352 0.5700091412963174 1.2720692807397587 chr6 171115067 93622621 0.5471325385975508 1.2634876426890123 chr7 159138663 85753107 0.5388577821594492 1.2882594871222877 chr8 146364022 85273069 0.5826094953854165 1.3716303374552286 chr9 141213431 71839427 0.5087294210704363 1.7447293271141386 chr10 135534747 80720608 0.5955713186965996 1.4598727911784393 chr11 135006516 80237362 0.5943221436808279 1.4791490452842018 chr12 133851895 74518778 0.5567256107954243 1.2846565645013546 chr13 115169878 49676985 0.4313366121652052 1.1077270970713395 chr14 107349540 74505149 0.6940425548167231 1.5964446898932825 chr15 102531392 51665592 0.5039002298925191 1.256517332618876 chr16 90354753 51426364 0.5691605841698223 1.6266284839662148 chr17 81195210 44685077 0.5503412947635704 1.3678168431162268 chr18 78077248 44737793 0.5729939789886037 2.001714284537958 chr19 59128983 25848781 0.43715923542943397 1.305701123855911 chr20 63025520 41745615 0.66236050095263 1.476749210281056 chr21 48129895 21212929 0.4407433051744659 1.6912179706234487 chr22 51304566 22003090 0.42887196433939234 1.187006771698823 chrMT 16571 207556 12.525254963490434 9.317444428677046 chrX 155270560 47875661 0.30833701507871164 0.8730597595593188 chrY 59373566 9003813 0.151646828826148 0.9281189169130538