BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716692.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 = 682,617 number of mapped reads = 618,314 (90.58%) number of supplementary alignments = 2,202 (0.32%) number of secondary alignments = 0 number of mapped bases = 35,445,787 bp number of sequenced bases = 35,434,306 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,045 duplication rate = 1.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5532 >>>>>>> ACTG content number of A's = 8,951,365 bp (25.26%) number of C's = 6,485,544 bp (18.3%) number of T's = 11,613,400 bp (32.77%) number of G's = 8,383,334 bp (23.66%) number of N's = 663 bp (0%) GC percentage = 41.96% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 185,213 number of insertions = 2,576 mapped reads with insertion percentage = 0.41% number of deletions = 7,127 mapped reads with deletion percentage = 1.14% homopolymer indels = 41% >>>>>>> Coverage mean coverageData = 0.0115X std coverageData = 0.1402X There is a 1.08% of reference with a coverageData >= 1X There is a 0.05% 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 2839318 0.011391417957590565 0.19915709324277225 chr2 243199373 3001663 0.012342396129450548 0.18878862682285757 chr3 198022430 2348584 0.01186019179746456 0.11495028709176015 chr4 191154276 2324462 0.012160136035879208 0.12551166886327925 chr5 180915260 2141414 0.01183655817646339 0.11319928843217911 chr6 171115067 2041380 0.011929867052560602 0.1236247846352455 chr7 159138663 1922302 0.012079415295829147 0.1570150227841137 chr8 146364022 1790338 0.012232090752466477 0.16013142251292914 chr9 141213431 1478042 0.010466723947809186 0.12108567145101917 chr10 135534747 1721113 0.012698684566843955 0.1572664422130445 chr11 135006516 1589639 0.011774535386129067 0.12794488463573508 chr12 133851895 1609687 0.012025881292155035 0.11546035679849345 chr13 115169878 1099751 0.009548946470187282 0.10297749786202334 chr14 107349540 1073717 0.010002064284579143 0.10481046607165703 chr15 102531392 1027523 0.010021545401431789 0.10523952365490284 chr16 90354753 1036067 0.011466657431956014 0.1155915475226974 chr17 81195210 979973 0.01206934497736997 0.11862166465222967 chr18 78077248 930931 0.011923204567865917 0.17283524918611798 chr19 59128983 747071 0.01263459917786849 0.1608637449588167 chr20 63025520 756129 0.011997187805828495 0.1157000776008549 chr21 48129895 463935 0.009639227345083549 0.11429391923544616 chr22 51304566 413585 0.008061368261062768 0.09384684527542313 chrMT 16571 6989 0.42176090760967955 0.7314298472375632 chrX 155270560 1964526 0.012652276130130528 0.12184245199614631 chrY 59373566 137648 0.002318338096788729 0.1040399589868562