BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716484.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 = 449,773 number of mapped reads = 405,711 (90.2%) number of supplementary alignments = 2,254 (0.5%) number of secondary alignments = 0 number of mapped bases = 23,540,530 bp number of sequenced bases = 23,533,589 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,096 duplication rate = 1.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0591 >>>>>>> ACTG content number of A's = 5,811,544 bp (24.69%) number of C's = 4,750,701 bp (20.19%) number of T's = 7,213,806 bp (30.65%) number of G's = 5,757,254 bp (24.46%) number of N's = 284 bp (0%) GC percentage = 44.65% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 116,818 number of insertions = 1,510 mapped reads with insertion percentage = 0.37% number of deletions = 4,339 mapped reads with deletion percentage = 1.06% homopolymer indels = 43.24% >>>>>>> Coverage mean coverageData = 0.0076X std coverageData = 0.1007X There is a 0.73% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 1901758 0.00762990275558832 0.14071377943064395 chr2 243199373 1973292 0.008113886050191421 0.11573613635113275 chr3 198022430 1559097 0.007873335359029782 0.09152305845010499 chr4 191154276 1459501 0.007635199329781145 0.0920861639203678 chr5 180915260 1415935 0.007826509494002883 0.09155935241503446 chr6 171115067 1345702 0.007864310394127947 0.0949331012269521 chr7 159138663 1289762 0.008104642678819038 0.1085635503665474 chr8 146364022 1182091 0.008076376857148678 0.10057356317306906 chr9 141213431 978782 0.006931224551862917 0.09231900380491367 chr10 135534747 1136017 0.008381739923858787 0.10336180264483535 chr11 135006516 1057908 0.007835977339049324 0.09673088829878455 chr12 133851895 1078686 0.008058802604176803 0.09322001818867892 chr13 115169878 711256 0.006175712020811553 0.0813328271609429 chr14 107349540 710398 0.006617615687966618 0.08453507416918776 chr15 102531392 693336 0.006762182649388004 0.08516255099162591 chr16 90354753 705600 0.007809218403817672 0.09218645537502618 chr17 81195210 680439 0.008380284994644388 0.0964186749882987 chr18 78077248 604058 0.007736671251527718 0.11287046935239779 chr19 59128983 527666 0.008923982338745789 0.11665321124145195 chr20 63025520 513134 0.008141686097948894 0.09361880163830477 chr21 48129895 323672 0.006724967922743234 0.08624584431603491 chr22 51304566 304788 0.005940757787523239 0.07960568209375975 chrMT 16571 2808 0.16945265825840322 0.3950019529209348 chrX 155270560 1312013 0.008449850377302691 0.0968505410332664 chrY 59373566 72831 0.0012266569941242875 0.04575407753059328