BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716780.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 = 4,679,964 number of mapped reads = 3,606,472 (77.06%) number of supplementary alignments = 82,431 (1.76%) number of secondary alignments = 0 number of mapped bases = 272,257,767 bp number of sequenced bases = 272,161,473 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 191,655 duplication rate = 3.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4042 >>>>>>> ACTG content number of A's = 71,589,238 bp (26.3%) number of C's = 55,001,843 bp (20.21%) number of T's = 82,567,798 bp (30.34%) number of G's = 62,967,815 bp (23.14%) number of N's = 34,779 bp (0.01%) GC percentage = 43.35% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 2,064,717 number of insertions = 23,498 mapped reads with insertion percentage = 0.64% number of deletions = 57,239 mapped reads with deletion percentage = 1.57% homopolymer indels = 40.6% >>>>>>> Coverage mean coverageData = 0.0879X std coverageData = 0.6593X There is a 6.78% of reference with a coverageData >= 1X There is a 1.33% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 21480480 0.08618024666827209 0.7533891986103473 chr2 243199373 23044965 0.09475750169799986 1.0065682697076763 chr3 198022430 18241372 0.09211770605986402 0.376071527460079 chr4 191154276 17306996 0.09053941330614022 0.4236383620121467 chr5 180915260 16714878 0.09239064742244518 0.3858960098182632 chr6 171115067 15695209 0.09172312687111299 0.4588961735535093 chr7 159138663 15044016 0.09453401025494351 0.9272940680194928 chr8 146364022 13980366 0.09551777690285117 0.8633420594215065 chr9 141213431 11459247 0.08114842135660595 0.7365502463397051 chr10 135534747 12848881 0.09480137960489202 0.6024993160020767 chr11 135006516 12324699 0.0912896604190571 0.7669406596750192 chr12 133851895 12381727 0.09250318794515386 0.3909143539422591 chr13 115169878 8775341 0.0761947581467439 0.34122477991275374 chr14 107349540 8238433 0.07674399908933005 0.4778657414478697 chr15 102531392 7831444 0.0763809390201198 0.3502210469472391 chr16 90354753 8041786 0.08900235718645592 0.44768639779042363 chr17 81195210 7365384 0.09071205062466123 0.4435469468339257 chr18 78077248 7531552 0.0964628261487905 1.4693490870819599 chr19 59128983 5423844 0.09172902567933564 0.6744639831277003 chr20 63025520 5729510 0.0909077783094848 0.40552033127407017 chr21 48129895 3607053 0.07494412776092696 0.38491844803401465 chr22 51304566 3102741 0.06047689790417485 0.3072152203915138 chrMT 16571 17659 1.0656568704363043 1.743918202929068 chrX 155270560 15393853 0.09914212327179087 0.5856952781128548 chrY 59373566 676331 0.011391113008101956 0.28412377840431285