BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524723.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 = 346,656
number of mapped reads = 318,028 (91.74%)
number of supplementary alignments = 1,080 (0.31%)
number of secondary alignments = 0
number of mapped bases = 18,928,177 bp
number of sequenced bases = 18,922,286 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 4,477
duplication rate = 1.02%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.975
>>>>>>> ACTG content
number of A's = 5,060,058 bp (26.74%)
number of C's = 3,394,445 bp (17.94%)
number of T's = 5,883,208 bp (31.09%)
number of G's = 4,581,823 bp (24.21%)
number of N's = 2,752 bp (0.01%)
GC percentage = 42.15%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 93,086
number of insertions = 1,519
mapped reads with insertion percentage = 0.47%
number of deletions = 3,675
mapped reads with deletion percentage = 1.15%
homopolymer indels = 41.84%
>>>>>>> Coverage
mean coverageData = 0.0061X
std coverageData = 0.092X
There is a 0.59% of reference with a coverageData >= 1X
There is a 0.01% of reference with a coverageData >= 2X
There is a 0% 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 1516960 0.0060860831315641935 0.13198985789715317
chr2 243199373 1586751 0.006524486393309904 0.10837771705940744
chr3 198022430 1274646 0.00643687687298858 0.08165668842052712
chr4 191154276 1234381 0.006457511837192698 0.08387225494555475
chr5 180915260 1142751 0.006316498674572836 0.08107295084503768
chr6 171115067 1098937 0.006422210616906108 0.08478542742767725
chr7 159138663 1042634 0.006551732811780629 0.10321978716985195
chr8 146364022 950869 0.006496603379756809 0.09552840434192147
chr9 141213431 800995 0.005672229577086049 0.08425125034914474
chr10 135534747 926232 0.0068339080604916756 0.09590867068311525
chr11 135006516 869513 0.006440526174307024 0.08598507448863382
chr12 133851895 858724 0.006415478839503916 0.08209385254072914
chr13 115169878 593830 0.005156122506268523 0.07334196799311861
chr14 107349540 559183 0.005208992977519978 0.07417072197709931
chr15 102531392 545096 0.005316381542932724 0.07422172137657328
chr16 90354753 544001 0.006020723669069186 0.0813542978002593
chr17 81195210 508096 0.006257709044659162 0.08125783503719078
chr18 78077248 515131 0.006597709488941003 0.11111100319980691
chr19 59128983 380917 0.006442136845140733 0.10702514580551876
chr20 63025520 400204 0.006349872242228227 0.0815303851777923
chr21 48129895 261986 0.005443311272546927 0.07710956499010574
chr22 51304566 209157 0.004076771646406676 0.06505082680713668
chrMT 16571 2759 0.1664956852332388 0.40422295635647315
chrX 155270560 1046358 0.006738933639448457 0.08499341311526265
chrY 59373566 58066 9.779773039065903E-4 0.04379935843000713