BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238635.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 = 2,610,594 number of mapped reads = 2,372,866 (90.89%) number of supplementary alignments = 22,164 (0.85%) number of secondary alignments = 0 number of mapped bases = 144,288,958 bp number of sequenced bases = 144,208,011 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 602,069 duplication rate = 20.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.2105 >>>>>>> ACTG content number of A's = 35,482,249 bp (24.6%) number of C's = 24,682,449 bp (17.12%) number of T's = 49,142,465 bp (34.08%) number of G's = 34,893,824 bp (24.2%) number of N's = 7,024 bp (0%) GC percentage = 41.31% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 870,248 number of insertions = 8,547 mapped reads with insertion percentage = 0.36% number of deletions = 47,767 mapped reads with deletion percentage = 1.99% homopolymer indels = 40.88% >>>>>>> Coverage mean coverageData = 0.0466X std coverageData = 0.588X There is a 2.48% of reference with a coverageData >= 1X There is a 1.06% of reference with a coverageData >= 2X There is a 0.52% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 30205370 0.12118473317665275 0.7007218489917928 chr2 243199373 3087197 0.012694099338816963 1.3121783322127336 chr3 198022430 23155064 0.1169315213433145 0.5862173255260946 chr4 191154276 6741176 0.03526563015519465 0.3117330924386138 chr5 180915260 4618251 0.02552715011436846 0.27087018295030113 chr6 171115067 6178310 0.036106171761017394 0.4942625682246523 chr7 159138663 7969858 0.05008121753542695 0.6524545619109898 chr8 146364022 2303171 0.015735909470976413 0.36297054026073367 chr9 141213431 12263049 0.08684052864631552 0.5623331535620426 chr10 135534747 2148422 0.015851448042323787 0.3633798547698012 chr11 135006516 9175485 0.06796327519480615 0.491330869539749 chr12 133851895 5527112 0.04129274374486816 0.370034111780216 chr13 115169878 4164570 0.03616023627289073 0.4084889879410598 chr14 107349540 4904676 0.0456888403993161 0.38826348991947496 chr15 102531392 600514 0.005856879422840568 0.2798248108191963 chr16 90354753 995885 0.011021943693432486 0.25612378221201626 chr17 81195210 1396120 0.017194610371720202 0.23208584726131137 chr18 78077248 4234816 0.05423879694120366 1.0001080755608625 chr19 59128983 838568 0.014182012905583036 0.3271981974917982 chr20 63025520 787216 0.012490432447046847 0.19550320545819538 chr21 48129895 866335 0.017999935383195827 0.24844635756017944 chr22 51304566 296693 0.0057829745601980145 0.1122782704596507 chrMT 16571 68865 4.155754028121417 4.643385992788136 chrX 155270560 11404529 0.07344939697518962 0.47605169553128124 chrY 59373566 357706 0.006024667610498585 0.21561831023740452