BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716933.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 = 500,650 number of mapped reads = 361,000 (72.11%) number of supplementary alignments = 417 (0.08%) number of secondary alignments = 0 number of mapped bases = 19,137,919 bp number of sequenced bases = 19,132,541 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,807 duplication rate = 4.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4238 >>>>>>> ACTG content number of A's = 4,109,732 bp (21.48%) number of C's = 3,728,801 bp (19.49%) number of T's = 6,374,424 bp (33.32%) number of G's = 4,919,220 bp (25.71%) number of N's = 364 bp (0%) GC percentage = 45.2% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 138,131 number of insertions = 1,426 mapped reads with insertion percentage = 0.39% number of deletions = 3,099 mapped reads with deletion percentage = 0.85% homopolymer indels = 38.72% >>>>>>> Coverage mean coverageData = 0.0062X std coverageData = 0.0911X There is a 0.57% of reference with a coverageData >= 1X There is a 0.04% 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 1562278 0.006267900130928861 0.09074996698090503 chr2 243199373 1629854 0.006701719580502373 0.12065707519488858 chr3 198022430 1218320 0.006152434347967551 0.08412640000688369 chr4 191154276 1155648 0.006045629866004148 0.08598544746641523 chr5 180915260 1152441 0.006370059662186595 0.08649756673630812 chr6 171115067 1058601 0.006186486196449317 0.09031102163054634 chr7 159138663 1027348 0.006455678215670318 0.09359398918415497 chr8 146364022 951158 0.006498577908715846 0.08949040485380533 chr9 141213431 779710 0.00552150028845344 0.08378193811272575 chr10 135534747 897653 0.0066230470035849925 0.09457743590186939 chr11 135006516 871951 0.006458584561948106 0.09148657237848817 chr12 133851895 870334 0.0065022164983170394 0.08885474661637713 chr13 115169878 580393 0.005039451374603349 0.07669296079966428 chr14 107349540 570144 0.005311098678205794 0.07945296537595488 chr15 102531392 570043 0.00555969239157506 0.08033580096799338 chr16 90354753 625424 0.006921871614213809 0.09628824227869315 chr17 81195210 585667 0.0072130732835101975 0.09943822411048503 chr18 78077248 494538 0.006333957877203869 0.09409857975933575 chr19 59128983 450088 0.0076119692435772145 0.10129526168197694 chr20 63025520 431834 0.0068517324410810095 0.09464654896671579 chr21 48129895 264592 0.005497456414563132 0.08775075174566928 chr22 51304566 260185 0.005071380976110392 0.07911051531578352 chrMT 16571 4910 0.296300766399131 0.6368657050869273 chrX 155270560 1055885 0.006800291053242804 0.08923276720594539 chrY 59373566 68920 0.0011607859295498606 0.04502331615829693