BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716247.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 = 1,495,929 number of mapped reads = 1,344,821 (89.9%) number of supplementary alignments = 5,254 (0.35%) number of secondary alignments = 0 number of mapped bases = 76,452,806 bp number of sequenced bases = 76,431,982 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,622 duplication rate = 2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4143 >>>>>>> ACTG content number of A's = 19,272,405 bp (25.22%) number of C's = 14,683,775 bp (19.21%) number of T's = 24,084,374 bp (31.51%) number of G's = 18,389,730 bp (24.06%) number of N's = 1,698 bp (0%) GC percentage = 43.27% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 379,203 number of insertions = 5,204 mapped reads with insertion percentage = 0.39% number of deletions = 12,050 mapped reads with deletion percentage = 0.89% homopolymer indels = 40.54% >>>>>>> Coverage mean coverageData = 0.0247X std coverageData = 0.2131X There is a 2.25% of reference with a coverageData >= 1X There is a 0.16% 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 6211828 0.024922016142138317 0.32034479878939465 chr2 243199373 6449135 0.026517893201969726 0.24257466371211195 chr3 198022430 5084249 0.02567511670268868 0.17243873477358815 chr4 191154276 4860810 0.02542872752686945 0.18502519603393208 chr5 180915260 4578298 0.02530631191641877 0.17165572644144403 chr6 171115067 4326640 0.025284973882516142 0.1789753620378582 chr7 159138663 4150532 0.02608122955010625 0.2332086495680728 chr8 146364022 3832278 0.026183196851477613 0.20291136470766677 chr9 141213431 3213828 0.022758656717292 0.215886243757868 chr10 135534747 3634191 0.02681372179785011 0.21439927758240207 chr11 135006516 3456636 0.02560347531670249 0.21511738684949125 chr12 133851895 3491469 0.02608456906792392 0.17502182407198855 chr13 115169878 2414703 0.020966445757631177 0.1549919440455889 chr14 107349540 2309002 0.021509193239207174 0.16620970694652845 chr15 102531392 2212239 0.02157621150798382 0.15771801426644624 chr16 90354753 2288414 0.025326990822497186 0.1831627300327854 chr17 81195210 2071484 0.025512391679262853 0.17783501628396026 chr18 78077248 2042832 0.026164241854426017 0.36796321584655334 chr19 59128983 1559335 0.02637175410238326 0.2504957209153926 chr20 63025520 1711696 0.027158776317910586 0.18383908868726104 chr21 48129895 1008950 0.0209630625622599 0.17077834203538667 chr22 51304566 937958 0.01828215445775333 0.14615191638730154 chrMT 16571 3891 0.2348077967533643 0.5597648418522715 chrX 155270560 4374029 0.028170369192975154 0.20001216330250826 chrY 59373566 228379 0.0038464760563648812 0.09393607536943831