BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237276.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 613,846 number of mapped reads = 457,344 (74.5%) number of supplementary alignments = 3,583 (0.58%) number of secondary alignments = 0 number of mapped bases = 30,626,829 bp number of sequenced bases = 30,610,822 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,565 duplication rate = 1.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4243 >>>>>>> ACTG content number of A's = 8,772,772 bp (28.66%) number of C's = 5,612,535 bp (18.34%) number of T's = 9,515,410 bp (31.09%) number of G's = 6,709,652 bp (21.92%) number of N's = 453 bp (0%) GC percentage = 40.25% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 289,786 number of insertions = 2,615 mapped reads with insertion percentage = 0.57% number of deletions = 9,002 mapped reads with deletion percentage = 1.94% homopolymer indels = 45.47% >>>>>>> Coverage mean coverageData = 0.0099X std coverageData = 0.1214X There is a 0.94% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% 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 2741894 0.01100055032560982 0.16340900586998086 chr2 243199373 2157397 0.008870898692654113 0.12498053020911332 chr3 198022430 2270389 0.011465312288107968 0.11031117012873816 chr4 191154276 1302399 0.006813339608474152 0.08823392996091153 chr5 180915260 1579700 0.00873171229447422 0.0966498810414603 chr6 171115067 3853384 0.022519256004499007 0.18422839257509163 chr7 159138663 1944730 0.012220348992123932 0.15137819669748015 chr8 146364022 1764915 0.012058393694592514 0.1492640700273795 chr9 141213431 1316268 0.009321124702366308 0.1142000393878788 chr10 135534747 1077229 0.00794799137375451 0.106999162092743 chr11 135006516 1340932 0.00993235022819195 0.11417050339492368 chr12 133851895 849352 0.006345461153164847 0.0823206266743967 chr13 115169878 922574 0.008010549425084917 0.09225421593144514 chr14 107349540 1166801 0.010869175592182324 0.1089980433588534 chr15 102531392 1087171 0.010603298938923993 0.10656775827599187 chr16 90354753 699587 0.007742669608094662 0.09558910140536349 chr17 81195210 769637 0.009478847335945064 0.10496651509716114 chr18 78077248 708837 0.009078662711062767 0.1549596451107491 chr19 59128983 458983 0.007762403084118663 0.11594738695432652 chr20 63025520 636515 0.010099321671602234 0.1040537761441105 chr21 48129895 521872 0.010842990619447643 0.10983101241053925 chr22 51304566 277344 0.005405834638577783 0.0754641800805565 chrMT 16571 26965 1.627240359664474 1.6719298646431209 chrX 155270560 1089670 0.007017878984915106 0.08877133840746278 chrY 59373566 62284 0.0010490190196761973 0.04052189486223735