BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524697.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 = 1,556,636
number of mapped reads = 1,438,906 (92.44%)
number of supplementary alignments = 5,773 (0.37%)
number of secondary alignments = 0
number of mapped bases = 85,280,805 bp
number of sequenced bases = 85,255,042 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 50,862
duplication rate = 2.54%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.9405
>>>>>>> ACTG content
number of A's = 21,754,458 bp (25.52%)
number of C's = 15,240,516 bp (17.88%)
number of T's = 27,971,772 bp (32.81%)
number of G's = 20,275,486 bp (23.78%)
number of N's = 12,810 bp (0.02%)
GC percentage = 41.66%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 427,102
number of insertions = 7,175
mapped reads with insertion percentage = 0.5%
number of deletions = 16,159
mapped reads with deletion percentage = 1.11%
homopolymer indels = 42.73%
>>>>>>> Coverage
mean coverageData = 0.0275X
std coverageData = 0.2696X
There is a 2.5% of reference with a coverageData >= 1X
There is a 0.18% of reference with a coverageData >= 2X
There is a 0.02% of reference with a coverageData >= 3X
There is a 0.01% 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 6819430 0.027359731232123992 0.4755731352971065
chr2 243199373 7199152 0.029601852633065792 0.3628588762062157
chr3 198022430 5728289 0.028927475539008384 0.18447858613503795
chr4 191154276 5558905 0.029080725350867902 0.20848879262231965
chr5 180915260 5137559 0.028397598964288586 0.18289736893622116
chr6 171115067 4945669 0.028902592195461083 0.2067666218031849
chr7 159138663 4688068 0.029459013363710363 0.31201186868777897
chr8 146364022 4345874 0.02969222859973061 0.30172179820291556
chr9 141213431 3598950 0.02548589021960666 0.22417163074691834
chr10 135534747 4116394 0.030371503183607963 0.2871671137327452
chr11 135006516 3900205 0.02888901303104511 0.2338211621844939
chr12 133851895 3850217 0.028764755254305514 0.18329355153788085
chr13 115169878 2663708 0.023128512821729307 0.16358446276918692
chr14 107349540 2546214 0.02371890927525167 0.17012215420958893
chr15 102531392 2396978 0.023377991396039955 0.1648398272025586
chr16 90354753 2484118 0.027492942180916594 0.19496948278095722
chr17 81195210 2290810 0.028213610137839414 0.19132510498770564
chr18 78077248 2249897 0.028816294857113817 0.39605568556647436
chr19 59128983 1758078 0.02973293147964341 0.36354158666133235
chr20 63025520 1786309 0.02834263009650694 0.18450536277428853
chr21 48129895 1111628 0.02309641440107027 0.18599739165207185
chr22 51304566 996784 0.019428758056349214 0.15013627329195672
chrMT 16571 30646 1.8493754148814194 1.6409817734392997
chrX 155270560 4788672 0.03084082391407618 0.2057235488853704
chrY 59373566 288251 0.004854870937009241 0.19014410596103104