Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A4 F81 I0 R1 263 75.1 3021180 96.0% 2900332 137.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 3,663,450 A→T 25.2% T1013S (ACA→TCA)  mdtF → anaerobic multidrug efflux transporter, ArcA‑regulated

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,663,4500AT25.2% 30.5 / 4.5 19T1013S (ACA→TCA) mdtFanaerobic multidrug efflux transporter, ArcA‑regulated
Reads supporting (aligned to +/- strand):  ref base A (6/8);  new base T (2/3);  total (8/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCAATCCTGATGACCTCTCTGGCCTTTATTCTCGGCGTGCTGCCGCTGGTTATCAGTCATGGTGCCGGTTCTGGCGCGCAAAACGCGGTAGGTACCGGCGTGATGGGCGGGATGTTTGCCGCAACAGTGCTGGCAATTTACTTCGTTCCGGTCTTTTTCGTTGTAGTGGAACATCTCTTTGCCCGCTTTAAAAAAGCGTAACGTGTAAATGAGAGTAAGGTTGAACATGAAGGTTCAGCCTTACTCTTTCCTGCTAACCATTCACCACT  >  NC_000913/3663327‑3663595
                                                                                                                           |                                                                                                                                                 
ccAATCCTGATGACCTCTCTGGCCTTTATTCTCGGCGTGCTGCCGCTGGTTATCAGTCATGGTGCCGGTTCTGGCGCGCAAAACGCGGTAGGTACCGGCGTGATGGGCGGGATGTTTGCCGCATCAGTGCTGGCAATTTACTTCGTTcc                                                                                                                          >  5:317595/1‑149 (MQ=255)
ccAATCCTGATGACCTCTCTGGCCTTTATTCTCGGCGTGCTGCCGCTGGTTATCAGTCATGGTGCCGGTTCTGGCGCGCAAAACGCGGTAGGTACCGGCGTGATGGGCGGGATGTTTGCCGCATCAGTGCTGGCAATTTACTTCGTTcc                                                                                                                          >  5:323114/1‑149 (MQ=255)
 cAATCCTGATGACCTCTCTGGCCTTTATTCTCGGCGTGCTGCCGCTGGTTATCAGTCATGGTGCCGGTTCTGGCGCGCAAAACGCGGTAGGTACCGGCGTGATGGGCGGGATGTTTGCCGCAACAGTGCTGGCAATTTACTTCGTTCCg                                                                                                                         <  5:9696/149‑1 (MQ=255)
    tCCTGATGACCTCTCTGGCCTTTATTCTCGGCGTGCTGCCGCTGGTTATCAGTCATGGTGCCGGTTCTGGCGCGCAAAACGCGGTAGGTACCGGCGTGATGGGCGGGATGTTTGCCGCAACAGTGCTGGCAATTTACTTCGTTCCGGTc                                                                                                                      >  5:68349/1‑149 (MQ=255)
                 tctGGCCTTTATTCTCGGCGTGCTGCCGCTGGTTATCAGTCATGGTGCCGGTTCTGGCGCGCAAAACGCGGTAGGTACCGGCGTGATGGGCGGGATGTTTGCCGCAACAGTGCTGGCAATTTACt                                                                                                                                 <  5:235707/125‑1 (MQ=255)
                 tctGGCCTTTATTCTCGGCGTGCTGCCGCTGGTTATCAGTCATGGTGCCGGTTCTGGCGCGCAAAACGCGGTAGGTACCGGCGTGATGGGCGGGATGTTTGCCGCAACAGTGCTGGCAATTTACt                                                                                                                                 >  6:235707/1‑125 (MQ=255)
                   tGGCCTTTATTCTCGGCGTGCTGCCGCTGGTTATCAGTCATGGTGCCGGTTCTGGCGCGCAAAACGCGGTAGGTACCGGCGTGATGGGCGGGATGTTTGCCGCAACAGTGCTGGCAATTTACtt                                                                                                                                >  8:103323/1‑124 (MQ=255)
                   tGGCCTTTATTCTCGGCGTGCTGCCGCTGGTTATCAGTCATGGTGCCGGTTCTGGCGCGCAAAACGCGGTAGGTACCGGCGTGATGGGCGGGATGTTTGCCGCAACAGTGCTGGCAATTTACtt                                                                                                                                <  7:103323/124‑1 (MQ=255)
                        tttATTCTCGGCGTGCTGCCGCTGGTTATCAGTCATGGTGCCGGTTCTGGCGCGCAAAACGCGGTAGGTACCGGCGTGATGGGCGGGATGTTTGCCGCAACAGTGCTGGCAATTTACTTCGTTCCGGTCTTTTTCGTTGTAGTGGAACa                                                                                                  >  6:19619/1‑149 (MQ=255)
                                 ggCGTGCTGCCGCTGGTTATCAGTCATGGTGCCGGTTCTGGCGCGCAAAACGCGGTAGGTACCGGCGTGATGGGCGGGATGTTTGCCGCATCAGTGCTGGCAATTTACTTCGTTCCGGTCTTTTTCGTTGTAGTGGAACATCTCttt                                                                                           <  6:323114/147‑1 (MQ=255)
                                 ggCGTGCTGCCGCTGGTTATCAGTCATGGTGCCGGTTCTGGCGCGCAAAACGCGGTAGGTACCGGCGTGATGGGCGGGATGTTTGCCGCATCAGTGCTGGCAATTTACTTCGTTCCGGTCTTTTTCGTTGTAGTGGAACATCTCttt                                                                                           <  6:317595/147‑1 (MQ=255)
                                       ctgcCGCTGGTTATCAGTCATGGTGCCGGTTCTGGCGCGCAAAACGCGGTAGGTACCGGCGTGATGGGCGGGATGTTTGCCGCAACAGTGCTGGCAATTTACTTCGTTCCGGTCTTTTTCGTTGTAGTGGAACATCTCTTTGCCCGCt                                                                                    <  6:68349/148‑1 (MQ=255)
                                                     cAGTCATGGTGACGGTTGTGGCGCGCAAAACGCGGTAGGTACCGGCGTGATGGGCGGGATGTTTGCCGCAACAGTGCTGGCAATTTACTTCGTTCCGGTCTTTTTCGttt                                                                                                            <  8:365317/110‑2 (MQ=255)
                                                                 cGGTTCTGGCGCGCAAAACGCGGTAGGTACCGGCGTGATGGGCGGGATGTTTGCCGCAACAGTGCTGGCAATTTACTTCGTTCCGGTCTTTTTCGTTGTAGTGGAACATCTCTTTGCCCGCTTTAAAAAAGCGTAACGTGTAAATgaga                                                         <  5:19619/149‑1 (MQ=255)
                                                                                 aaCGCGGTAGGTACCGGCGTGATGGGCGGGATGTTTGCCGCAACAGTGCTGGCAATTTACTTCGTTCCGGTCTTTTTCGTTGTAGTGGAACATCTCTTTGCCCGCTTTAAAAAAGCGTAACGTGTAAATGAGAGTAAGGTTGAACATGa                                         <  8:353943/149‑1 (MQ=255)
                                                                                      ggtaggtaCCGGCGTGATGGGCGGGATGTTTGCCGCAACAGTGCTGGCAATTTACTTCGTTCCGGGCTTTTTCGTTGTAGTGGAACATCTCTTTGCCCGCTTTAAAAAAGCGTAACGTGTAAATGAGAGTAAGGTTGAACATGAAGGt                                     >  3:234986/1‑148 (MQ=255)
                                                                                          ggttgcGGCGTTTTGGGCGGGATGTTTGCCGCTTCTGTGCTGGCAATTTACTTCGTTCCGTTCTTTTTCGTTGTAGTGGAACATCTCTTTGACCTCTTTAATAATGCGTAACGTGTAATTGAGAGTAAGGTTGAACATGAAGGTTCAg                                 <  4:234986/143‑1 (MQ=255)
                                                                                           gtaCCGGCGTGATGGGCGGGATGTTTGCCGCAACAGTGCTGGCAATTTACTTCGTTCCGGTCTTTTTCGTTGTAGTGGAACATCTCTTTGCCCGCTTTAAAAAAGCGTAACGTGTAAATGAGAGTAAGGTTGAACATGAAGGTTCAGcc                               <  5:373596/149‑1 (MQ=255)
                                                                                                                        gCAACAGTGCTGGCAATTTACTTCGTTCCGGTCTTTTTCGTTGTAGTGGAACATCTCTTTGCCCGCTTTAAAAAAGCGTAACGTGTAAATGAGAGTAAGGTTGAACATGAAGGTTCAGCCTTACTCTTTCCTGCTAACCATTCACCACt  >  1:253569/1‑149 (MQ=255)
                                                                                                                          aaCAGTGCTGGCAATTTACTTCGTTCCGGTCTTTTTCGTTGTAGTGGAACATCTCTTTGCCCGCTTTAAAAAAGCGTAACGTGTAAATGAGAGTAAGGTTGAACATGAAg                                       >  4:228491/1‑110 (MQ=255)
                                                                                                                           |                                                                                                                                                 
CCAATCCTGATGACCTCTCTGGCCTTTATTCTCGGCGTGCTGCCGCTGGTTATCAGTCATGGTGCCGGTTCTGGCGCGCAAAACGCGGTAGGTACCGGCGTGATGGGCGGGATGTTTGCCGCAACAGTGCTGGCAATTTACTTCGTTCCGGTCTTTTTCGTTGTAGTGGAACATCTCTTTGCCCGCTTTAAAAAAGCGTAACGTGTAAATGAGAGTAAGGTTGAACATGAAGGTTCAGCCTTACTCTTTCCTGCTAACCATTCACCACT  >  NC_000913/3663327‑3663595

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A