BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524294.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 = 1,993,617
number of mapped reads = 1,827,138 (91.65%)
number of supplementary alignments = 7,410 (0.37%)
number of secondary alignments = 0
number of mapped bases = 106,354,180 bp
number of sequenced bases = 106,325,367 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 60,299
duplication rate = 2.27%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.0826
>>>>>>> ACTG content
number of A's = 27,016,016 bp (25.41%)
number of C's = 19,100,971 bp (17.96%)
number of T's = 33,312,118 bp (31.33%)
number of G's = 26,881,183 bp (25.28%)
number of N's = 15,079 bp (0.01%)
GC percentage = 43.25%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 538,244
number of insertions = 8,454
mapped reads with insertion percentage = 0.46%
number of deletions = 18,821
mapped reads with deletion percentage = 1.02%
homopolymer indels = 40.02%
>>>>>>> Coverage
mean coverageData = 0.0344X
std coverageData = 0.3214X
There is a 3.08% of reference with a coverageData >= 1X
There is a 0.25% of reference with a coverageData >= 2X
There is a 0.03% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0.01% 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 8947310 0.03589684135631502 0.6428502788689096
chr2 243199373 6888487 0.028324443912114857 0.3936256320185838
chr3 198022430 7545320 0.03810336031125363 0.21390343490464964
chr4 191154276 5608394 0.029339620945753785 0.20237048716393408
chr5 180915260 6290565 0.03477078163555689 0.20323609178422922
chr6 171115067 6780338 0.039624435877408735 0.23752685687240152
chr7 159138663 4884152 0.03069117150996801 0.39390512232191055
chr8 146364022 11188503 0.07644298678810561 0.39016454610180684
chr9 141213431 4345163 0.030770182193222115 0.24016671837459824
chr10 135534747 5419448 0.039985672456377554 0.31107558583679323
chr11 135006516 5140065 0.03807271791237098 0.27253675838342684
chr12 133851895 4213862 0.031481526653021986 0.19703757218259477
chr13 115169878 2682076 0.02328799896792458 0.16667954331955465
chr14 107349540 2284455 0.021280529008321787 0.17120693887584684
chr15 102531392 3209901 0.03130651927557952 0.19719509509941124
chr16 90354753 3262532 0.03610802853946156 0.22208993749392228
chr17 81195210 3164199 0.03897026684209574 0.23512240788132358
chr18 78077248 2522432 0.032306876389905544 0.4507200426548598
chr19 59128983 1792282 0.030311395682215605 0.4388479452118416
chr20 63025520 2386631 0.037867692325267606 0.21315148978872414
chr21 48129895 1532399 0.0318388186801571 0.20689926628427147
chr22 51304566 748595 0.014591196424895203 0.13200144479354528
chrMT 16571 7841 0.4731760304145797 0.7851271638549094
chrX 155270560 5219604 0.03361618583716063 0.22586228930642238
chrY 59373566 289626 0.004878029391059314 0.1312450887999015