BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867844.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 = 1,934,947 number of mapped reads = 1,789,115 (92.46%) number of supplementary alignments = 7,984 (0.41%) number of secondary alignments = 0 number of mapped bases = 105,529,327 bp number of sequenced bases = 105,497,073 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,760 duplication rate = 3.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8235 >>>>>>> ACTG content number of A's = 27,417,580 bp (25.99%) number of C's = 18,840,875 bp (17.86%) number of T's = 32,977,634 bp (31.26%) number of G's = 26,246,394 bp (24.88%) number of N's = 14,590 bp (0.01%) GC percentage = 42.74% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 529,794 number of insertions = 7,576 mapped reads with insertion percentage = 0.42% number of deletions = 20,286 mapped reads with deletion percentage = 1.13% homopolymer indels = 42.7% >>>>>>> Coverage mean coverageData = 0.0341X std coverageData = 0.3203X There is a 3.04% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8405791 0.03372425298791933 0.5840019648094954 chr2 243199373 8964539 0.036860863946388545 0.43193325344810635 chr3 198022430 6941042 0.03505179691007731 0.205720395750806 chr4 191154276 6871937 0.03594969018637072 0.24269533910677007 chr5 180915260 6394890 0.03534743282573289 0.20876213121630502 chr6 171115067 6047619 0.03534241084684846 0.23600685228231055 chr7 159138663 5852647 0.036777027591340265 0.3760292760791423 chr8 146364022 5360561 0.03662485443314751 0.3511450128101867 chr9 141213431 4449539 0.03150931868513272 0.26955228638039264 chr10 135534747 5154769 0.03803282268273242 0.33651504530199494 chr11 135006516 4809637 0.035625221230062704 0.26815247532515474 chr12 133851895 4772988 0.03565872563851263 0.21054535877873795 chr13 115169878 3288967 0.028557527863318565 0.18587072950571487 chr14 107349540 3159388 0.029430848050210554 0.1990306977668183 chr15 102531392 3038582 0.029635626130970698 0.19033806181113969 chr16 90354753 3031243 0.03354824067749928 0.21892093340693655 chr17 81195210 2855121 0.03516366297962651 0.22254059164808349 chr18 78077248 2769028 0.035465235659945395 0.4863650496619555 chr19 59128983 2184676 0.036947633616495654 0.43332971023812034 chr20 63025520 2258272 0.03583107287333766 0.21328362097333053 chr21 48129895 1387106 0.028820050407340387 0.21881702265847527 chr22 51304566 1253183 0.024426344431020038 0.17065192739255944 chrMT 16571 36815 2.221652284110796 1.8029058640192892 chrX 155270560 5877265 0.037851766619505976 0.2358907004033575 chrY 59373566 363722 0.0061259921629096695 0.22520229216698248