BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717025.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 = 845,470 number of mapped reads = 768,159 (90.86%) number of supplementary alignments = 4,211 (0.5%) number of secondary alignments = 0 number of mapped bases = 43,904,009 bp number of sequenced bases = 43,892,167 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,485 duplication rate = 1.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1469 >>>>>>> ACTG content number of A's = 10,686,604 bp (24.35%) number of C's = 8,125,920 bp (18.51%) number of T's = 13,423,379 bp (30.58%) number of G's = 11,655,383 bp (26.55%) number of N's = 881 bp (0%) GC percentage = 45.07% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 220,941 number of insertions = 2,686 mapped reads with insertion percentage = 0.35% number of deletions = 7,029 mapped reads with deletion percentage = 0.91% homopolymer indels = 41.1% >>>>>>> Coverage mean coverageData = 0.0142X std coverageData = 0.1456X There is a 1.33% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% 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 3566943 0.014310668457672569 0.19869305130855802 chr2 243199373 3707897 0.015246326313513974 0.16107771112714225 chr3 198022430 2916190 0.014726564056405125 0.12650734797074956 chr4 191154276 2798925 0.014642230655619757 0.13282485617284195 chr5 180915260 2603478 0.014390593695634078 0.12594661032443813 chr6 171115067 2468140 0.014423861342379628 0.1291775462054886 chr7 159138663 2389253 0.015013655104039677 0.16029520452260754 chr8 146364022 2204247 0.015060032990894442 0.13983663473622676 chr9 141213431 1857860 0.013156397283485026 0.14486921315569903 chr10 135534747 2112687 0.01558778871664548 0.14930850826912015 chr11 135006516 1982608 0.014685276375845444 0.14573773767309206 chr12 133851895 2002142 0.014957890584963328 0.12921293438585313 chr13 115169878 1357289 0.011785104087719881 0.11284807968883374 chr14 107349540 1311843 0.012220294562976236 0.12013020228322281 chr15 102531392 1275483 0.012439926690939688 0.11725616871132358 chr16 90354753 1323584 0.014648747919215716 0.13135421412681084 chr17 81195210 1230812 0.01515867746385532 0.13306024601641253 chr18 78077248 1183658 0.015160088634271535 0.23975544419609873 chr19 59128983 924685 0.015638439105235415 0.16041938303970205 chr20 63025520 944500 0.014985992975543875 0.12967863843556052 chr21 48129895 596721 0.012398136335015898 0.12338516214032844 chr22 51304566 547132 0.010664391937356998 0.10783129921288838 chrMT 16571 836 0.05044958059260153 0.23146701904998554 chrX 155270560 2461219 0.015851163285557805 0.14109945227102846 chrY 59373566 135877 0.0022885100079722345 0.06449496423717513