BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716671.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,844,556 number of mapped reads = 2,595,107 (91.23%) number of supplementary alignments = 16,037 (0.56%) number of secondary alignments = 0 number of mapped bases = 151,299,392 bp number of sequenced bases = 151,258,646 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 192,540 duplication rate = 5.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.843 >>>>>>> ACTG content number of A's = 39,141,746 bp (25.88%) number of C's = 30,668,128 bp (20.28%) number of T's = 45,893,371 bp (30.34%) number of G's = 35,554,354 bp (23.51%) number of N's = 1,047 bp (0%) GC percentage = 43.78% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 735,911 number of insertions = 12,612 mapped reads with insertion percentage = 0.48% number of deletions = 26,137 mapped reads with deletion percentage = 1% homopolymer indels = 40.4% >>>>>>> Coverage mean coverageData = 0.0489X std coverageData = 0.3972X There is a 3.87% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 17536678 0.07035761006188225 0.649396669800919 chr2 243199373 15611049 0.06419033407623136 0.5662519949294881 chr3 198022430 9447818 0.04771084770548468 0.2657096847973315 chr4 191154276 6420273 0.03358686572096352 0.27096687346918624 chr5 180915260 10446790 0.05774410627384335 0.2933761710274714 chr6 171115067 5660567 0.03308047093246324 0.2502053502815764 chr7 159138663 10381932 0.0652382758801989 0.6264153524519125 chr8 146364022 6805860 0.04649954208008851 0.3847790637550612 chr9 141213431 4269646 0.03023541011477867 0.3012974588289887 chr10 135534747 6857985 0.0505994599303749 0.34818248519596 chr11 135006516 6560284 0.04859235090549259 0.3676323158801066 chr12 133851895 5294453 0.0395545614053503 0.2459862275856221 chr13 115169878 4418867 0.03836825285167012 0.24002548289478837 chr14 107349540 3153611 0.029377033194553048 0.22552175516773906 chr15 102531392 6788543 0.06620941028480332 0.3158511831483206 chr16 90354753 4611805 0.05104108911680606 0.29115680291121804 chr17 81195210 5827069 0.07176616699433377 0.3595687779052166 chr18 78077248 4901851 0.06278206680645301 0.6463539045635331 chr19 59128983 2466815 0.04171921915179904 0.4614425073273648 chr20 63025520 4086315 0.0648358791803701 0.3182309407351169 chr21 48129895 1957883 0.04067914546665851 0.27012160898760845 chr22 51304566 1834871 0.03576428265663528 0.23056609054853744 chrMT 16571 3234 0.19516021966085328 0.4854314635956129 chrX 155270560 5593857 0.036026513976635366 0.26460962776618363 chrY 59373566 361336 0.006085805929190779 0.15627323719317604