BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524616.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 = 1,669,888
number of mapped reads = 1,561,501 (93.51%)
number of supplementary alignments = 3,405 (0.2%)
number of secondary alignments = 0
number of mapped bases = 91,026,357 bp
number of sequenced bases = 90,997,725 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 68,918
duplication rate = 3.46%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.3308
>>>>>>> ACTG content
number of A's = 21,652,503 bp (23.79%)
number of C's = 16,903,038 bp (18.58%)
number of T's = 29,207,164 bp (32.1%)
number of G's = 23,234,459 bp (25.53%)
number of N's = 561 bp (0%)
GC percentage = 44.11%
>>>>>>> Mismatches and indels
general error rate = 0.0046
number of mismatches = 410,352
number of insertions = 4,878
mapped reads with insertion percentage = 0.31%
number of deletions = 16,673
mapped reads with deletion percentage = 1.06%
homopolymer indels = 46.38%
>>>>>>> Coverage
mean coverageData = 0.0294X
std coverageData = 0.2569X
There is a 2.59% of reference with a coverageData >= 1X
There is a 0.26% of reference with a coverageData >= 2X
There is a 0.04% 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 9625844 0.03861913748251002 0.4367685812341275
chr2 243199373 8092171 0.03327381522484435 0.3060918041782669
chr3 198022430 5515951 0.027855182869940542 0.18635738646260486
chr4 191154276 4080227 0.02134520391267627 0.18558503529579032
chr5 180915260 5581710 0.030852621276944797 0.1949020466493306
chr6 171115067 5992598 0.03502086698186548 0.22139952929654444
chr7 159138663 5489753 0.034496664082191014 0.3313483069855722
chr8 146364022 8016713 0.054772428978482154 0.33777842500226823
chr9 141213431 3360948 0.023800483963880178 0.22484873129250452
chr10 135534747 3836942 0.028309655530621973 0.25330205397502165
chr11 135006516 4646894 0.03441977570919614 0.2543531285930843
chr12 133851895 2813976 0.02102305686445455 0.16775536374693475
chr13 115169878 2170227 0.018843703212049943 0.1529624333530336
chr14 107349540 1696694 0.01580532156914692 0.14551646224307163
chr15 102531392 2399576 0.023403329977222977 0.1760945618166859
chr16 90354753 2751113 0.03044790571227614 0.20235109693750192
chr17 81195210 2251000 0.027723310279017692 0.19182868147721294
chr18 78077248 2392041 0.030636850827529167 0.3448323329264362
chr19 59128983 1930978 0.03265704739078634 0.31793676480040434
chr20 63025520 1736060 0.02754534988366617 0.18855779603406952
chr21 48129895 806044 0.016747262797893077 0.15751577297676786
chr22 51304566 1889020 0.03681972477849243 0.21438707171583238
chrMT 16571 3862 0.2330577514935731 0.5294951877087837
chrX 155270560 3734973 0.024054611511673558 0.19455361710996388
chrY 59373566 211042 0.0035544774251895193 0.10709485073067915