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
A21 F26 I1 R1 16 35.0 1240938 93.0% 1154072 143.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913_3_pae_tpiA 2,795,396 C→A Q382K (CAG→AAG)  gabP → gamma‑aminobutyrate transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_tpiA2,795,3960CA97.6% 130.3 / NA 42Q382K (CAG→AAG) gabPgamma‑aminobutyrate transporter
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base A (24/17);  minor base G (0/1);  total (24/18)
Fisher's exact test for biased strand distribution p-value = 4.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCGGTGTTACTCTCCACCGGCGCGGCATTCTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAG  >  NC_000913_3_pae_tpiA/2795260‑2795536
                                                                                                                                        |                                                                                                                                            
ggCGGTGTTACTCGCCACCGGCGCGGCATTCGTGACGGGGGTGGTGAACTATTACGGGCCTGCGAAGGTATTTAAATGGCTGATCGAGAGCGCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCTTTTCAAAGTTGCGGATgc                                                                                                                                  <  2:545279/149‑1 (MQ=255)
     tgtTACTCTCCACCGGCGCGGCATTCTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCaaa                                                                                                                             >  1:364464/1‑149 (MQ=255)
           tctcCACCGGCGCGGCATTCTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTg                                                                                                                       >  1:477909/1‑149 (MQ=255)
           tctcCACCGGCGCGGCATTCTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTg                                                                                                                       >  1:516/1‑149 (MQ=255)
             tcCACCGGCGCGGCATTCTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCg                                                                                                                     >  2:556666/1‑149 (MQ=255)
                  cGGCGCGGCATTCTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAg                                                                                                                >  1:58282/1‑149 (MQ=255)
                   ggCGCGGCATTCTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAga                                                                                                               <  1:443728/149‑1 (MQ=255)
                     cgcgGCATTCTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAgaag                                                                                                             <  2:75641/149‑1 (MQ=255)
                         gcgttCTTGACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGTGCAAAATTCTGCGAGCAgaaggaag                                                                                                         <  1:24082/146‑1 (MQ=255)
                         gCATTCTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAgaaggaag                                                                                                         >  2:130823/1‑149 (MQ=255)
                              ctgcaCGGGGGTTGTGAACTAGTACGCGCCTGCGAAGGTATTTCAATTTCTGATCGACAGCTCCGGCGCTATCGGCCGGGTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGGGaaa                                                                                                    <  2:11965/145‑1 (MQ=255)
                              cTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCTGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGAGGATGCGCAAAATCCTGCGAGCAGAAAGAAGCGaca                                                                                                    >  2:584005/1‑147 (MQ=255)
                              cTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGaaa                                                                                                    >  1:420474/1‑149 (MQ=255)
                                          ggtgAACTGTTGCGCGACGGCGTAGGTAGTTCAATTTCTGATCGACAGCCTCGTCGTTATCGCGCTGCTGGTTTAGTCAGTCATCGCCGATTCAGAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGTAGCGAAATTCGCTGGCGaa                                                                                        <  2:99687/149‑1 (MQ=255)
                                          ggggAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGTGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGaa                                                                                        <  2:99409/146‑1 (MQ=255)
                                             gAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAAtgt                                                                                     <  2:396305/149‑1 (MQ=255)
                                                   ttctgggcCTGGCAAGGCTTTTAAATTTCGGATCGAAAGCTCCTGCGCAACCGCCCTGCTGGTTTATTTAGTCATGGGCGTTTCAAAGTTGCGGAGTCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCttt                                                                               <  2:192919/143‑1 (MQ=255)
                                                       gcgcCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATcc                                                                           >  2:32776/1‑149 (MQ=255)
                                                                      tttAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCt                                                            >  2:418456/1‑149 (MQ=255)
                                                                      ttgaaaaTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCt                                                            >  2:77617/4‑149 (MQ=255)
                                                                       ttAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGTCTTTCTCCGTGTGTCCCGTGGCtt                                                           >  1:51590/1‑148 (MQ=255)
                                                                       ttAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTa                                                           <  2:357633/149‑1 (MQ=255)
                                                                           aTTTCTGATCGACAGCTCCGGCGCGCTCGCGCTGCTGGTTTAGTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAACTTCGCTTGCGAATGTGGCTTTATCCGTGGCCCACCTGGCTAGTCa                                                       >  2:613205/1‑149 (MQ=255)
                                                                                   tCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCttt                                               >  1:130298/1‑149 (MQ=255)
                                                                                   tCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCttt                                               >  1:215159/1‑149 (MQ=255)
                                                                                         gCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTAcc                                         >  1:283210/1‑149 (MQ=255)
                                                                                          cTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCt                                        <  2:138677/149‑1 (MQ=255)
                                                                                           tCCGGCGCTATCGCCCTGCTGGTTTATTTAGTAATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCCCACCTGGCTAGTCATCGGCATTATTACCtt                                       >  2:183970/1‑149 (MQ=255)
                                                                                                cgcTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTgtgt                                  >  2:193333/1‑149 (MQ=255)
                                                                                                  cTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTg                                <  2:477909/149‑1 (MQ=255)
                                                                                                    aTCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGt                              >  2:124433/1‑149 (MQ=255)
                                                                                                     tCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGGTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTa                             <  1:325761/149‑1 (MQ=255)
                                                                                                      cGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAg                            <  1:32776/149‑1 (MQ=255)
                                                                                                       gCCGTGCTGGTTGAGTTAGGCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGt                           <  2:303917/149‑1 (MQ=255)
                                                                                                           tgctgGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATg                       >  2:452649/1‑149 (MQ=255)
                                                                                                           tgctgGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCAGTGACTCACCTGGCTAGTCATCGGCCTTATTACCTTTGATTTCGTAGTGAta                       >  2:424117/1‑148 (MQ=255)
                                                                                                                gTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAACGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTAtt                  >  1:569512/1‑149 (MQ=255)
                                                                                                                     tttaGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATtccgtt             <  2:420474/149‑2 (MQ=255)
                                                                                                                           cATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTCTGTTGGTAGTGATGCTATTCCGTCCGgcgc       <  2:130298/149‑1 (MQ=255)
                                                                                                                            aTCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCa      >  2:570019/1‑149 (MQ=255)
                                                                                                                               gCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACa   <  1:193333/149‑1 (MQ=255)
                                                                                                                                ccGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAg  >  1:427527/1‑149 (MQ=255)
                                                                                                                                        |                                                                                                                                            
GGCGGTGTTACTCTCCACCGGCGCGGCATTCTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAG  >  NC_000913_3_pae_tpiA/2795260‑2795536

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A