BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6013311.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,091,726
number of mapped reads = 1,808,828 (86.48%)
number of supplementary alignments = 24,182 (1.16%)
number of secondary alignments = 0
number of mapped bases = 119,240,815 bp
number of sequenced bases = 119,190,856 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 165,261
duplication rate = 7.29%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.4058
>>>>>>> ACTG content
number of A's = 32,607,299 bp (27.36%)
number of C's = 22,459,635 bp (18.84%)
number of T's = 37,376,024 bp (31.36%)
number of G's = 26,720,092 bp (22.42%)
number of N's = 27,806 bp (0.02%)
GC percentage = 41.26%
>>>>>>> Mismatches and indels
general error rate = 0.0084
number of mismatches = 990,132
number of insertions = 7,837
mapped reads with insertion percentage = 0.43%
number of deletions = 29,209
mapped reads with deletion percentage = 1.6%
homopolymer indels = 45.27%
>>>>>>> Coverage
mean coverageData = 0.0385X
std coverageData = 0.3924X
There is a 2.51% of reference with a coverageData >= 1X
There is a 0.81% of reference with a coverageData >= 2X
There is a 0.29% of reference with a coverageData >= 3X
There is a 0.11% of reference with a coverageData >= 4X
There is a 0.04% of reference with a coverageData >= 5X
There is a 0.02% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0.01% 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 8683746 0.034839415706009416 0.6625138895119064
chr2 243199373 12231377 0.05029362061718802 0.4857455081973795
chr3 198022430 7642268 0.03859294121378068 0.2819418600154852
chr4 191154276 7375240 0.03858265770628118 0.28425285305533654
chr5 180915260 6554752 0.036231061990016765 0.28155146664778297
chr6 171115067 6244681 0.036494045261367895 0.32500797422235317
chr7 159138663 7474694 0.04696969208544877 0.5392685399337914
chr8 146364022 6706007 0.04581731841176105 0.3879334761227292
chr9 141213431 4259117 0.030160849218372154 0.335674191079066
chr10 135534747 5635088 0.04157670357402888 0.38974318690502974
chr11 135006516 5075965 0.037597926014178454 0.3252522624677638
chr12 133851895 5822389 0.04349874165023962 0.3010654810190506
chr13 115169878 2979503 0.025870505827921428 0.23093760389353213
chr14 107349540 3870714 0.03605710839562051 0.2825408981274213
chr15 102531392 3386889 0.033032702803839825 0.2621472326908034
chr16 90354753 3952346 0.04374253560296933 0.31245844128420774
chr17 81195210 3153344 0.03883657668968404 0.3205387649431434
chr18 78077248 2942035 0.03768107964051192 0.5551813925594434
chr19 59128983 2439026 0.041249246583524024 0.5692219276085033
chr20 63025520 2752367 0.043670674990067514 0.30636876916208633
chr21 48129895 2049575 0.04258424000301684 0.30559546182708924
chr22 51304566 1246876 0.024303411902948366 0.21932349072265175
chrMT 16571 209864 12.664534427614507 9.249557708547243
chrX 155270560 6301048 0.04058108633085371 0.3137385237955255
chrY 59373566 251904 0.004242696152021591 0.09996213618179811