BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068932.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 = 2,864,569 number of mapped reads = 2,460,668 (85.9%) number of supplementary alignments = 13,694 (0.48%) number of secondary alignments = 0 number of mapped bases = 161,212,103 bp number of sequenced bases = 161,138,377 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 93,956 duplication rate = 2.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1743 >>>>>>> ACTG content number of A's = 42,978,004 bp (26.67%) number of C's = 28,157,359 bp (17.47%) number of T's = 52,757,698 bp (32.74%) number of G's = 36,853,544 bp (22.87%) number of N's = 391,772 bp (0.24%) GC percentage = 40.34% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 1,557,978 number of insertions = 15,467 mapped reads with insertion percentage = 0.62% number of deletions = 44,043 mapped reads with deletion percentage = 1.77% homopolymer indels = 47.63% >>>>>>> Coverage mean coverageData = 0.0521X std coverageData = 0.5782X There is a 4.5% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 18496597 0.0742088301557331 1.2194969918200396 chr2 243199373 12499696 0.05139690882344503 0.5253917602584851 chr3 198022430 9836810 0.04967523123516866 0.3463907567820202 chr4 191154276 6135988 0.032099663833834405 0.23850273250162035 chr5 180915260 6922601 0.038264328835500114 0.22112212214852714 chr6 171115067 10885789 0.06361677665707836 0.4171003505624544 chr7 159138663 10086458 0.06338156806055358 0.5499693821832509 chr8 146364022 9419303 0.06435531677313432 0.6483773762699012 chr9 141213431 8534416 0.06043629093609375 0.5363372115539089 chr10 135534747 11718254 0.08645940808079275 1.0971898698496272 chr11 135006516 5295818 0.039226388154479895 0.43022638184669726 chr12 133851895 8006889 0.05981901862502582 0.2866861853776179 chr13 115169878 3929938 0.03412296746550344 0.2004620501604051 chr14 107349540 4377211 0.04077531212523128 0.29078763376345085 chr15 102531392 3131791 0.03054470381129713 0.19332831757703747 chr16 90354753 2984227 0.03302789173691836 0.2950955913782667 chr17 81195210 3999771 0.04926116947046507 0.2966018617137152 chr18 78077248 3614334 0.04629176991484126 0.9484091022327624 chr19 59128983 3180944 0.05379669729817609 0.7108926482914368 chr20 63025520 1990317 0.031579541112869834 0.23333492943270975 chr21 48129895 2342390 0.04866808872115761 0.2928206949198708 chr22 51304566 1076258 0.020977820960419 0.1661320105904984 chrMT 16571 277881 16.769114718484097 12.6257234831999 chrX 155270560 12015513 0.07738436056390857 0.38681895598123867 chrY 59373566 452909 0.0076281252839015936 0.15904862335769612