BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716149.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 = 669,928
number of mapped reads = 481,009 (71.8%)
number of supplementary alignments = 586 (0.09%)
number of secondary alignments = 0
number of mapped bases = 25,486,251 bp
number of sequenced bases = 25,479,692 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 27,798
duplication rate = 4.93%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.6198
>>>>>>> ACTG content
number of A's = 5,298,975 bp (20.8%)
number of C's = 4,985,091 bp (19.56%)
number of T's = 8,467,018 bp (33.23%)
number of G's = 6,728,185 bp (26.41%)
number of N's = 423 bp (0%)
GC percentage = 45.97%
>>>>>>> Mismatches and indels
general error rate = 0.0071
number of mismatches = 178,261
number of insertions = 1,439
mapped reads with insertion percentage = 0.3%
number of deletions = 3,887
mapped reads with deletion percentage = 0.8%
homopolymer indels = 40.05%
>>>>>>> Coverage
mean coverageData = 0.0082X
std coverageData = 0.1109X
There is a 0.74% of reference with a coverageData >= 1X
There is a 0.06% 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 2518784 0.01010542717965786 0.11792717018916372
chr2 243199373 2191609 0.00901157339743635 0.17059643162900767
chr3 198022430 1750094 0.008837857408375404 0.10387046077379805
chr4 191154276 1600005 0.008370228662841945 0.10266597649016898
chr5 180915260 1459543 0.008067550520613906 0.09942474629265476
chr6 171115067 1051414 0.006144485219410866 0.09936623511048627
chr7 159138663 1266233 0.007956790487802451 0.10199136521250453
chr8 146364022 1525978 0.010425909175958556 0.11733684415741565
chr9 141213431 1110812 0.007866192274586119 0.10066806470463642
chr10 135534747 1313759 0.009693152708655589 0.11539282090534879
chr11 135006516 1143133 0.008467243166248362 0.10792067095985722
chr12 133851895 1217341 0.0090946863322331 0.10697138361131936
chr13 115169878 460628 0.00399955273027206 0.07138309097309593
chr14 107349540 1153588 0.010746091692614613 0.1176771651499331
chr15 102531392 495149 0.004829242930789431 0.0772886649163689
chr16 90354753 681894 0.007546852571220022 0.10043614773433414
chr17 81195210 1020478 0.012568204454425328 0.12805742898356673
chr18 78077248 628482 0.008049489654143548 0.10533012313066983
chr19 59128983 689744 0.011665074638608278 0.14052589616301886
chr20 63025520 653764 0.010373004459146073 0.12021316816812508
chr21 48129895 358433 0.00744720095483275 0.09905898151357807
chr22 51304566 298445 0.005817123567520286 0.08951919916624934
chrMT 16571 2094 0.12636533703457847 0.37454486007298027
chrX 155270560 822161 0.005295021799367504 0.08165554132297742
chrY 59373566 72686 0.001224214829879007 0.042985963530590664