BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716311.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 = 2,028,678 number of mapped reads = 1,896,953 (93.51%) number of supplementary alignments = 39,546 (1.95%) number of secondary alignments = 0 number of mapped bases = 150,362,337 bp number of sequenced bases = 150,292,419 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,548 duplication rate = 3.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5136 >>>>>>> ACTG content number of A's = 39,614,910 bp (26.36%) number of C's = 30,100,196 bp (20.03%) number of T's = 45,528,151 bp (30.29%) number of G's = 35,038,491 bp (23.31%) number of N's = 10,671 bp (0.01%) GC percentage = 43.34% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 957,803 number of insertions = 13,942 mapped reads with insertion percentage = 0.72% number of deletions = 36,657 mapped reads with deletion percentage = 1.9% homopolymer indels = 42.31% >>>>>>> Coverage mean coverageData = 0.0486X std coverageData = 0.4674X There is a 4.12% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 14716293 0.059042151794678976 1.0552263364837204 chr2 243199373 12323578 0.05067273754854623 0.4621504199778344 chr3 198022430 9569609 0.04832588409302926 0.24697263111116904 chr4 191154276 9392040 0.04913329796504264 0.3286083530811648 chr5 180915260 8831235 0.04881420727029881 0.25121852241526677 chr6 171115067 8329730 0.04867911485550247 0.2748324082029451 chr7 159138663 7868550 0.04944461547977188 0.5272388749458409 chr8 146364022 7361152 0.050293452580853514 0.49564888922083766 chr9 141213431 6032420 0.04271845784980609 0.35356963356733817 chr10 135534747 6942082 0.05121994288298631 0.45019450585969417 chr11 135006516 8437559 0.06249742049487449 0.5177891647278298 chr12 133851895 6462125 0.0482781734244405 0.250272361455571 chr13 115169878 5374408 0.04666504899831534 0.24619148701720506 chr14 107349540 4417685 0.04115234215256069 0.25172341399126974 chr15 102531392 4144032 0.04041720217745605 0.22661103917973185 chr16 90354753 3378970 0.037396704520901075 0.2458679676058978 chr17 81195210 4584762 0.05646591713969334 0.32456525439369377 chr18 78077248 3923804 0.050255408592270054 0.6235650405708549 chr19 59128983 2889488 0.048867540982397754 0.6844948273834603 chr20 63025520 3067698 0.04867390225419798 0.2634149669545329 chr21 48129895 1955876 0.0406374458120052 0.26414058949207325 chr22 51304566 1695991 0.033057311117298996 0.20440229565259677 chrMT 16571 13085 0.7896324904954438 1.0774496931270092 chrX 155270560 8192198 0.05276079380405403 0.30834368071978213 chrY 59373566 457967 0.00771331470978179 0.25716398439563265