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
A3 F1 I1 R1 781 46.9 2231650 93.5% 2086592 109.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,712,518 (C)6→7 intergenic (+360/‑251) nth → / → dtpA DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,712,5121.C97.6% 143.3 / ‑3.4 42intergenic (+354/‑257)nth/dtpADNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base C (19/22);  total (20/22)
Fisher's exact test for biased strand distribution p-value = 4.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

GAATCAGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑C‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGACTTGTCTGA  >  NC_000913/1712374‑1712645
                                                                                                                                           |                                                                                                                                      
gAATCAGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCa                                                                                                                                         <  2:717111/139‑1 (MQ=255)
     aGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑c‑cccc                                                                                                                                  <  1:496674/139‑1 (MQ=255)
     aGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑c‑cccc                                                                                                                                  <  1:314417/139‑1 (MQ=255)
                 ttaaaaTTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTAGTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTcagtgca                                                                                                                       >  2:644780/4‑139 (MQ=255)
                          acacacGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGaaaaaa                                                                                                              >  1:1077373/1‑139 (MQ=255)
                                gCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCa                                                                                                                                         >  2:339269/1‑107 (MQ=255)
                                gCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCa                                                                                                                                         <  1:339269/107‑1 (MQ=255)
                                               cTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGaa                                                                                         <  2:951645/139‑1 (MQ=255)
                                                         ttACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCTTCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGGTACGTTTATTGAAAAAATTAACg                                                                               <  2:981067/139‑1 (MQ=255)
                                                         ttACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                               <  2:923371/139‑1 (MQ=255)
                                                            cacTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTcagtg                                                                                                                         <  1:453892/94‑1 (MQ=255)
                                                            cacTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTcagtg                                                                                                                         >  2:453892/1‑94 (MQ=255)
                                                            cacTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTaa                                                                                 <  2:841775/134‑1 (MQ=255)
                                                            cacTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTaa                                                                                 >  1:841775/1‑134 (MQ=255)
                                                               tGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGAt                                                                         >  2:89564/1‑139 (MQ=255)
                                                                 gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATaa                                                                       >  2:175490/1‑139 (MQ=255)
                                                                 gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CACCCCCTCTCAGTGCAGTGAAAAAATATACCGTTACGTTTTTTGAAAAATTTAACGCTGGATaa                                                                       >  1:1088375/1‑139 (MQ=255)
                                                                           aGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCgg                                                             >  1:273148/1‑139 (MQ=255)
                                                                             aaaCTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGaa                                                           <  1:175490/139‑1 (MQ=255)
                                                                                   gACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTg                                                     >  1:359409/1‑139 (MQ=255)
                                                                                          tcACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTccc                                              <  1:89564/139‑1 (MQ=255)
                                                                                           cACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTcccc                                             >  1:69782/1‑139 (MQ=255)
                                                                                             cTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGc                                           <  2:1077373/139‑1 (MQ=255)
                                                                                               aGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                         <  2:441648/139‑1 (MQ=255)
                                                                                                  aaaaaCGGTAAATTTCAGAACATGTCCCCGGTAACCCATGACC‑CCCCCTCTCAGTGCAGTGAAAACGTCTGCCGTTACGTTTTTTGAATAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAg                                      <  2:1088375/139‑1 (MQ=255)
                                                                                                    aaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGtt                                    <  2:69782/139‑1 (MQ=255)
                                                                                                     aaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTta                                   >  2:648920/1‑139 (MQ=255)
                                                                                                     aaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTta                                   <  1:648920/139‑1 (MQ=255)
                                                                                                      aCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGa                                                                          <  2:226324/99‑1 (MQ=255)
                                                                                                      aCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGa                                                                          >  1:226324/1‑99 (MQ=255)
                                                                                                        gCTAAATAGCAGAACATATCGCCGTTAAGCCATCa                                                                                                                                         <  2:654576/35‑1 (MQ=255)
                                                                                                        gCTAAATAGCAGAACATATCGCCGTTAAGCCATCa                                                                                                                                         >  1:654576/1‑35 (MQ=255)
                                                                                                            aaTAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTaa                            <  1:164233/139‑1 (MQ=255)
                                                                                                            aaTAGCAGAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTaa                            <  2:359409/139‑1 (MQ=255)
                                                                                                                   gAACATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGatta                     <  2:273148/139‑1 (MQ=255)
                                                                                                                    aaCATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGattat                    >  2:304002/1‑139 (MQ=255)
                                                                                                                      cATATCGCCGTTCAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGcc                                          <  1:699268/115‑1 (MQ=255)
                                                                                                                      cATATCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGcc                                          >  2:699268/1‑115 (MQ=255)
                                                                                                                        tatCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAg                                      >  2:790726/1‑117 (MQ=255)
                                                                                                                        tatCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAg                                      <  1:790726/117‑1 (MQ=255)
                                                                                                                        tatCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACa                <  1:644780/139‑1 (MQ=255)
                                                                                                                         atCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTccc                                              >  1:103362/1‑108 (MQ=255)
                                                                                                                         atCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTccc                                              <  2:103362/108‑1 (MQ=255)
                                                                                                                         atCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACa                          <  1:10538/128‑1 (MQ=255)
                                                                                                                         atCGCCGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACa                          >  2:10538/1‑128 (MQ=255)
                                                                                                                              cGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAg                                      >  1:263188/1‑111 (MQ=255)
                                                                                                                              cGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAg                                      <  2:263188/111‑1 (MQ=255)
                                                                                                                              cGTTAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGAc          >  2:594842/1‑139 (MQ=255)
                                                                                                                                ttAAGCCATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGACtt        >  2:241345/1‑139 (MQ=255)
                                                                                                                                      cATCACC‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGACTTGTCTGa  <  1:304002/139‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                      
GAATCAGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑C‑CCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGACTTGTCTGA  >  NC_000913/1712374‑1712645

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A