BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716151.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 = 1,190,562 number of mapped reads = 842,868 (70.8%) number of supplementary alignments = 1,133 (0.1%) number of secondary alignments = 0 number of mapped bases = 44,203,447 bp number of sequenced bases = 44,191,129 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,871 duplication rate = 6.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.001 >>>>>>> ACTG content number of A's = 9,454,801 bp (21.4%) number of C's = 8,107,533 bp (18.35%) number of T's = 14,307,354 bp (32.38%) number of G's = 12,320,690 bp (27.88%) number of N's = 751 bp (0%) GC percentage = 46.23% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 323,874 number of insertions = 2,521 mapped reads with insertion percentage = 0.3% number of deletions = 7,348 mapped reads with deletion percentage = 0.87% homopolymer indels = 40.19% >>>>>>> Coverage mean coverageData = 0.0143X std coverageData = 0.1628X There is a 1.24% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 4322273 0.0173410721412004 0.18890566546647755 chr2 243199373 3834164 0.01576551761915932 0.28363566717229716 chr3 198022430 2959909 0.014947342076349634 0.1388531812738511 chr4 191154276 2800773 0.01465189823951414 0.1431272848924761 chr5 180915260 2676418 0.014793765876908338 0.13732654210397 chr6 171115067 1896838 0.011085160607160327 0.147817453804335 chr7 159138663 2527339 0.0158813637890121 0.1654995875849115 chr8 146364022 2738928 0.018713123365795455 0.1642838981463994 chr9 141213431 1957021 0.013858603860421747 0.14382049664621296 chr10 135534747 2226726 0.01642918918792094 0.16313192913944455 chr11 135006516 1916038 0.014192189064415231 0.1501753897380531 chr12 133851895 2103063 0.015711865715461105 0.14373586709788402 chr13 115169878 766550 0.006655820196319041 0.0946917996301475 chr14 107349540 1416511 0.013195315042803165 0.13282114050036037 chr15 102531392 874261 0.008526764173844436 0.10510511016786798 chr16 90354753 1218406 0.013484691834639845 0.13988219547527628 chr17 81195210 1741302 0.02144587100643006 0.1704425240182328 chr18 78077248 1194816 0.015302998384369285 0.15747306506032346 chr19 59128983 1221421 0.020656891731082202 0.19948079959394954 chr20 63025520 1184369 0.018791895727318077 0.16393165567414414 chr21 48129895 617629 0.012832544097592567 0.13806592466747045 chr22 51304566 504716 0.009837642910769384 0.11571396773223355 chrMT 16571 4049 0.24434252609981294 0.5180138327642836 chrX 155270560 1362605 0.008775681623097128 0.11009012007171046 chrY 59373566 137322 0.002312847437864857 0.07343991716779827