BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524408.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 = 1,823,156
number of mapped reads = 1,684,699 (92.41%)
number of supplementary alignments = 6,360 (0.35%)
number of secondary alignments = 0
number of mapped bases = 98,778,832 bp
number of sequenced bases = 98,749,932 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 69,208
duplication rate = 2.92%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.9679
>>>>>>> ACTG content
number of A's = 24,829,255 bp (25.14%)
number of C's = 18,402,193 bp (18.64%)
number of T's = 31,670,579 bp (32.07%)
number of G's = 23,836,319 bp (24.14%)
number of N's = 11,586 bp (0.01%)
GC percentage = 42.77%
>>>>>>> Mismatches and indels
general error rate = 0.005
number of mismatches = 478,415
number of insertions = 7,607
mapped reads with insertion percentage = 0.45%
number of deletions = 17,931
mapped reads with deletion percentage = 1.06%
homopolymer indels = 44.1%
>>>>>>> Coverage
mean coverageData = 0.0319X
std coverageData = 0.3329X
There is a 2.86% of reference with a coverageData >= 1X
There is a 0.23% 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 7802502 0.03130384176655672 0.706491581559652
chr2 243199373 8349112 0.034330318771010976 0.36257908357397367
chr3 198022430 6713339 0.03390191202077462 0.19951460422083817
chr4 191154276 6343369 0.0331845519375146 0.22593856798683803
chr5 180915260 6104896 0.03374450557680983 0.2002547777997833
chr6 171115067 5478061 0.03201390208379488 0.22147524119581669
chr7 159138663 5500919 0.034566829306590316 0.45854750224581786
chr8 146364022 5098975 0.034837625601734284 0.2897487976968771
chr9 141213431 4184672 0.029633668485825545 0.2757501559128399
chr10 135534747 4788045 0.03532706635000396 0.2940335195500632
chr11 135006516 4550316 0.0337044176445528 0.2777107280999882
chr12 133851895 4484612 0.03350428471707479 0.20519540104260808
chr13 115169878 3154467 0.027389687779299374 0.18011209461880817
chr14 107349540 3089191 0.028776937469876442 0.19429170634947554
chr15 102531392 2783533 0.027148105040844465 0.1799223422462416
chr16 90354753 2653305 0.029365417002468037 0.2021683866983568
chr17 81195210 2675522 0.03295172215208262 0.22049423034369614
chr18 78077248 2732964 0.035003334133908 0.5175017183020153
chr19 59128983 1927083 0.032591174449930926 0.4740954878758151
chr20 63025520 1957778 0.03106325818493842 0.19706536270577787
chr21 48129895 1341719 0.027877039831481036 0.20980746588027838
chr22 51304566 1101771 0.02147510613382832 0.15847965653470597
chrMT 16571 70731 4.26836038863074 2.8744130201311027
chrX 155270560 5582396 0.03595270088547372 0.23211136128835302
chrY 59373566 309554 0.005213666970921032 0.15677670304528296