BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068940.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 = 3,453,032 number of mapped reads = 2,909,492 (84.26%) number of supplementary alignments = 18,445 (0.53%) number of secondary alignments = 0 number of mapped bases = 193,342,477 bp number of sequenced bases = 193,255,500 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 136,939 duplication rate = 3.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2886 >>>>>>> ACTG content number of A's = 53,594,520 bp (27.73%) number of C's = 33,496,372 bp (17.33%) number of T's = 64,052,855 bp (33.14%) number of G's = 41,632,751 bp (21.54%) number of N's = 479,002 bp (0.25%) GC percentage = 38.88% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 1,981,195 number of insertions = 17,303 mapped reads with insertion percentage = 0.59% number of deletions = 52,982 mapped reads with deletion percentage = 1.8% homopolymer indels = 48.33% >>>>>>> Coverage mean coverageData = 0.0625X std coverageData = 0.5681X There is a 5.13% of reference with a coverageData >= 1X There is a 0.8% of reference with a coverageData >= 2X There is a 0.15% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 20377824 0.0817563620032064 1.104459372760315 chr2 243199373 14428130 0.059326345384944724 0.48549442505338464 chr3 198022430 11817866 0.05967943126442798 0.28575904935182767 chr4 191154276 9778759 0.0511563706793564 0.302979955626556 chr5 180915260 11762534 0.06501681505473889 0.29822274579807917 chr6 171115067 14219557 0.08309938598218239 0.43939685196220774 chr7 159138663 12527460 0.07872040498417408 0.6940770752212176 chr8 146364022 12193014 0.08330608733886802 1.231234262232865 chr9 141213431 7912682 0.05603349443439272 0.4143397170594118 chr10 135534747 13032128 0.09615340928035229 0.5374625581521796 chr11 135006516 5994804 0.04440381233154702 0.3980902179530124 chr12 133851895 9362854 0.06994935708605396 0.3133436279939608 chr13 115169878 4767455 0.04139498176771534 0.23694833091434367 chr14 107349540 6215780 0.05790225090857399 0.3021795249219757 chr15 102531392 3409299 0.03325127001104208 0.21131200839668368 chr16 90354753 3839183 0.04249010563948971 0.2751269719678133 chr17 81195210 3915378 0.048221785496952344 0.2761571072752303 chr18 78077248 4988078 0.0638864474321636 0.828588598239415 chr19 59128983 2807159 0.04747517812034751 0.6390079097407602 chr20 63025520 1452426 0.023045045879827728 0.2146801234692715 chr21 48129895 2986357 0.06204786027478348 0.3133504167829389 chr22 51304566 1434298 0.027956537045845005 0.19696939324859028 chrMT 16571 373348 22.530203367328465 11.348502543216147 chrX 155270560 13232183 0.08522016665619032 0.38835459850069226 chrY 59373566 513921 0.008655720628267468 0.18675005014840576