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
A2 F28 I1 R1 155 60.3 2039550 99.3% 2025273 138.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,008,546 T→C V346A (GTT→GCT)  ygeX → 2,3‑diaminopropionate ammonia‑lyase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,008,5460TC97.7% 143.0 / ‑4.4 43V346A (GTT→GCT) ygeX2,3‑diaminopropionate ammonia‑lyase
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (20/22);  total (20/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

AACTGCGCCACCCAATTCATCTCCTGCCAGGACAGCGTTGCCGCATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGTTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGATGCCGTGGTGCTGGTTATCAGCACTGAAGGCGACACCGACGTGAAGCACTACCGCGAAG  >  NC_000913/3008419‑3008671
                                                                                                                               |                                                                                                                             
aaCTGCGCCACCCAATTCATCTCCTGCCAGGACAGCGTTGCCGCATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGt                                                                                                                   <  2:722435/140‑1 (MQ=255)
  cTGCGCCACCCAATTCATCTCCTGCCAGGACAGCGTTGCCGCATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGt                                                                                                                   >  2:70442/1‑138 (MQ=255)
  cTGCGCCACCCAATTCATCTCCTGCCAGGACAGCGTTGCCGCATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGt                                                                                                                   <  1:70442/138‑1 (MQ=255)
   tGCGCCACCCAATTCATCTCCTGCCAGGACAGCGTTGCCGCATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCa                                                                                                                <  2:153676/140‑1 (MQ=255)
   tGCGCCACCCAATTCATCTCCTGCCAGGACAGCGTTGCCGCATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCa                                                                                                                >  1:769963/1‑140 (MQ=255)
    gcgcCACCCAATTCATCTCCTGCCAGGACAGCGTTGCCGCATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCAt                                                                                                               >  1:847423/1‑140 (MQ=255)
     cgcCACCCAATTCATCTCCTGCCAGGACAGCGTTGCCGCATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCAtt                                                                                                              >  1:513565/1‑140 (MQ=255)
     cgcCACCCAATTCATCTCCTGCCAGGACAGCGTTGCCGCATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCAGTTTGGGCGCTCTCGCAGCGGTTCAtt                                                                                                              >  2:978355/1‑140 (MQ=255)
       ccACCCAATTCATCTCCTGCCAGGACAGCGTTGCCGCATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTAt                                                                                                            >  2:660391/1‑140 (MQ=255)
           ccAATTCATCTCCTGCCAGGACAGCGTTGCCGCATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGTTCTCGCAGCGGTTCATTATCAcc                                                                                                        <  1:707150/140‑1 (MQ=255)
               ttCATCTCCTGCCAGGACAGCGTTGCCGCATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCa                                                                                                    <  2:513565/140‑1 (MQ=255)
                    ctcCTGCCAGGACAGCGTTGCCGCATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTc                                                                                               >  1:942410/1‑140 (MQ=255)
                       cTGCCAGGACAGCGTTGCCGCATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCaaa                                                                                            >  1:233911/1‑140 (MQ=255)
                        tGCCAGGACAGCGTTGCCGCATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAg                                                                                           >  1:355603/1‑140 (MQ=255)
                          ccAGGACAGCGTTGCCGCATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGcc                                                                                         >  1:893799/1‑140 (MQ=255)
                                   cGTTGCCGCATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGaaa                                                                                >  1:656393/1‑140 (MQ=255)
                                   cGTTGCCGCATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGaaa                                                                                >  2:848664/1‑140 (MQ=255)
                                   cGTTGCCGCATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGaaa                                                                                >  1:880658/1‑140 (MQ=255)
                                           cATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGgcg                                                                        <  1:244580/140‑1 (MQ=255)
                                           cATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGgcg                                                                        <  2:359657/140‑1 (MQ=255)
                                           cATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCAGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGgcg                                                                        <  1:978355/140‑1 (MQ=255)
                                           cATTAGGTATGCGCGTGCTGGGTAATCCGTACGACAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGgcg                                                                        <  2:708107/140‑1 (MQ=255)
                                                      cgcgTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGa                                                             >  2:276085/1‑140 (MQ=255)
                                                      cgcgTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGa                                                             >  1:235842/1‑140 (MQ=255)
                                                        cgTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGATg                                                           <  2:769963/140‑1 (MQ=255)
                                                           gCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGATGCCg                                                        <  1:131610/140‑1 (MQ=255)
                                                           gCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGATGCCg                                                        <  1:276085/140‑1 (MQ=255)
                                                                gTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGATGCCgtggtg                                                   <  2:992802/140‑1 (MQ=255)
                                                                 tAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGATGCCGTGGTGc                                                  >  1:930505/1‑140 (MQ=255)
                                                                   aTCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGATGCCGTGGTGCTg                                                <  2:205517/140‑1 (MQ=255)
                                                                   aTCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGATGCCGTGGTGCTg                                                <  1:809046/140‑1 (MQ=255)
                                                                        tACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGATGCCGTGGTGCTGGTTAt                                           <  2:880658/140‑1 (MQ=255)
                                                                         aCGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGATGCCGTGGTGCTGGTTATc                                          >  1:817447/1‑140 (MQ=255)
                                                                           ggCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGATGCCGTGGTGCTGGTTATCAg                                        <  2:272529/140‑1 (MQ=255)
                                                                           ggCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGATGCCGTGGTGCTGGTTATCAg                                        <  2:837328/140‑1 (MQ=255)
                                                                                cGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGATGCCgtgg                                                     <  2:590346/122‑1 (MQ=255)
                                                                                cGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGATGCCgtgg                                                     >  1:590346/1‑122 (MQ=255)
                                                                                cGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGATGCCGTGGTGCTGGTTATCAGCACTg                                   <  2:177059/140‑1 (MQ=255)
                                                                                               ctcCGGTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGATGCCGTGGTGCTGGTTATCAGCACTGAAGGCGACACCGACg                    <  2:133083/140‑1 (MQ=255)
                                                                                                    gTGAATCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGATGCCGTGGTGCTGGTTATCAGCACTGAAGGCGACACCGACGTGAAg               >  2:613370/1‑140 (MQ=255)
                                                                                                        aTCCGGCGCTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGATGCCGTGGTGCTGGTTATCAGCACTGAAGGCGACACCGACGTGAAGCACt           >  1:64370/1‑140 (MQ=255)
                                                                                                                cTGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGATGCCGTGGTGCTGGTTATCAGCACTGAAGGCGACACCGACGTGAAGCACTACCGCGaa   <  2:233911/140‑1 (MQ=255)
                                                                                                                 tGTCGGTTTGGGCGCTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGATGCCGTGGTGCTGGTTATCAGCACTGAAGGCGACACCGACGTGAAGCACTACCGCGAAg  <  2:218760/140‑1 (MQ=255)
                                                                                                                               |                                                                                                                             
AACTGCGCCACCCAATTCATCTCCTGCCAGGACAGCGTTGCCGCATTAGGTATGCGCGTGCTGGGTAATCCGTACGGCAACGACCCGCGCATCATCTCCGGTGAATCCGGCGCTGTCGGTTTGGGCGTTCTCGCAGCGGTTCATTATCACCCGCAACGTCAAAGCCTGATGGAAAAACTGGCGCTGAACAAAGATGCCGTGGTGCTGGTTATCAGCACTGAAGGCGACACCGACGTGAAGCACTACCGCGAAG  >  NC_000913/3008419‑3008671

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A