BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716574.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 = 798,782 number of mapped reads = 751,415 (94.07%) number of supplementary alignments = 17,454 (2.19%) number of secondary alignments = 0 number of mapped bases = 58,459,989 bp number of sequenced bases = 58,437,379 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,127 duplication rate = 2.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5728 >>>>>>> ACTG content number of A's = 14,886,024 bp (25.47%) number of C's = 12,170,036 bp (20.83%) number of T's = 16,747,108 bp (28.66%) number of G's = 14,631,856 bp (25.04%) number of N's = 2,355 bp (0%) GC percentage = 45.86% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 373,221 number of insertions = 5,709 mapped reads with insertion percentage = 0.75% number of deletions = 10,659 mapped reads with deletion percentage = 1.39% homopolymer indels = 37.96% >>>>>>> Coverage mean coverageData = 0.0189X std coverageData = 0.187X There is a 1.71% of reference with a coverageData >= 1X There is a 0.13% 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 4715100 0.018917104322881507 0.2370031458024711 chr2 243199373 4884670 0.020085043558068713 0.2085349532063843 chr3 198022430 3720298 0.01878725556493777 0.1464900234608743 chr4 191154276 3713251 0.01942541426590949 0.20720473808020812 chr5 180915260 3473736 0.019200901018521045 0.14968925275447056 chr6 171115067 3257110 0.019034618383429673 0.15364557998064685 chr7 159138663 3167082 0.019901398819719883 0.20799392390343913 chr8 146364022 2947272 0.020136587938257122 0.18701262335672902 chr9 141213431 2435571 0.017247445818379697 0.16969158882268914 chr10 135534747 2919370 0.021539642524289363 0.2818563086674577 chr11 135006516 2668487 0.019765616349954544 0.1868667637947022 chr12 133851895 2589562 0.019346472457487433 0.1509167982022924 chr13 115169878 1739715 0.01510564246668734 0.1319080696166635 chr14 107349540 1738474 0.016194517461369653 0.14554176084817308 chr15 102531392 1729305 0.016866102822440956 0.14005573791700293 chr16 90354753 1876965 0.020773284610716605 0.1641861064921916 chr17 81195210 1682960 0.020727331082707957 0.16784588655853455 chr18 78077248 1540199 0.019726604605736105 0.24820178676316196 chr19 59128983 1318139 0.022292603950248898 0.20765036956732685 chr20 63025520 1321839 0.020973075668395912 0.16442396363033576 chr21 48129895 798672 0.01659409396176742 0.17799687159561295 chr22 51304566 801792 0.01562808269345851 0.1380667981032402 chrMT 16571 2395 0.14452959990344577 0.4215580132602355 chrX 155270560 3193567 0.020567756051114907 0.16195029881874481 chrY 59373566 224458 0.00378043656667009 0.17887697612210693