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
A23 F43 I0 R1 23 38.0 846132 95.3% 806363 140.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,643,957 C→T 56.5% A38A (GCG→GCA)  cfiB_2 ← 2‑oxoglutarate carboxylase small subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,643,9570CT56.5% 4.2 / 34.2 32A38A (GCG→GCA) cfiB_22‑oxoglutarate carboxylase small subunit
Reads supporting (aligned to +/- strand):  ref base C (7/7);  new base T (8/10);  total (15/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.85e-01

ATAACCCGGATGAACGCCATCACAACCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGCGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCTTTTTCATTATTTCACCTTAAATA  >  USA300TCH1516_ALE/1643828‑1644086
                                                                                                                                 |                                                                                                                                 
aTAACCCGGATGAACGCCATCACAACCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATc                                                                                                                        >  1:303818/1‑141 (MQ=255)
  aaCCCGGATGAACGCCATCACAACCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATTCTTCATCAGCAATTTGCGTATGTAGTGCCTCTTTATccc                                                                                                                      >  2:252686/1‑141 (MQ=255)
       ggATTAACTCCATCACAACCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGCGCATCTTTATCCCCTTCa                                                                                                                 <  2:218286/141‑1 (MQ=255)
       ggATGAACGCCATCACAACCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCa                                                                                                                 <  1:386691/141‑1 (MQ=255)
                 cATCACAACCTGGAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGAttt                                                                                                       <  2:74486/141‑2 (MQ=255)
                  aTCACAACCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGc                                                                                                      <  1:346105/141‑1 (MQ=255)
                    aacaACCAGTAGAAGTTGGAATAGATAAGATGTTGGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCaa                                                                                                    <  2:262816/140‑1 (MQ=255)
                       aagcTGTAGAATGTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATTTTTATACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGCGCATCTTTATCCCCTTCAGAATAGATTGCAACAg                                                                                                 <  2:327861/138‑1 (MQ=255)
                       aaCCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGCGCATCTTTATCCCCTTCAGAATAGATTGCAACAg                                                                                                 <  2:187175/141‑1 (MQ=255)
                               gAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGCGCATCTTTATCCCCTTCAGAATAGATTGCACCAGTTTGGATg                                                                                         >  2:404944/1‑141 (MQ=255)
                                  gTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGCGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCt                                                                                      <  1:198109/141‑1 (MQ=255)
                                    tGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATGTGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCGCCTTCAGGATAGATTGCAACAGTTTGGATGCCTaa                                                                                    >  1:4187/1‑141 (MQ=255)
                                            attagagGTTCGGAAGATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGCGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGAc                                                                            <  2:42934/138‑1 (MQ=255)
                                                    ttCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGa                                                                    <  1:380180/141‑1 (MQ=255)
                                                           tatTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGAAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATcc                                                             <  2:56543/141‑1 (MQ=255)
                                                              ttAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGCGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTaa                                                          >  1:394993/1‑141 (MQ=255)
                                                                          cTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGCGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCAc                                              >  1:237814/1‑141 (MQ=255)
                                                                                  aaaGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGttt                                      <  2:234563/141‑1 (MQ=255)
                                                                                       gggACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGCGCATCTTTATCCCCTTCAGAATAGATTGCAACCGTTTGGATGCCTAAATCACGACAAGCGCGAATAACCCTAACTGCCAGCTCACCGCGTTTCGCAAt                                 >  2:212496/1‑141 (MQ=255)
                                                                                       gggACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGCGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAAt                                 <  2:354781/141‑1 (MQ=255)
                                                                                        ggACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCAAGACAAGCGCGAATAAACCTAACTGCGATTTCACCGCGGTTTGCAAtt                                >  2:135685/1‑141 (MQ=255)
                                                                                        ggACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGCGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTACGATTTCACCGCGGGTTGCAAtt                                >  2:351980/1‑141 (MQ=255)
                                                                                         gACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTa                               >  1:410124/1‑141 (MQ=255)
                                                                                         gACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGCGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCCCCGGGGTTTGCAATTa                               >  1:196574/1‑141 (MQ=255)
                                                                                            cTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTCAACAAAGGCAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTaaaa                            >  1:307949/1‑141 (MQ=255)
                                                                                                      tGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCttttcctt                  >  2:139932/1‑137 (MQ=255)
                                                                                                       gCTTCATCATCAATTTGAGTATGTAGCGCATCTTTATCCCCTTTAGCATAGATTGCAAAAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCGTAACTGCGATTTCAGCGCGGTTTGCAATTAAAACCTTTTTCatt                 <  1:187206/141‑1 (MQ=255)
                                                                                                                 cAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCTTTTTCATTATTTCACCtt       >  2:113716/1‑141 (MQ=255)
                                                                                                                   aTTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCTATTTCACCGCGGTTTGCAATTAAAACCTTTTTCATTATTTCACCTTaa     <  2:73674/141‑1 (MQ=255)
                                                                                                                     ttGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCTTTTTCATTATTTCACCTTAAAt   <  1:252686/141‑1 (MQ=255)
                                                                                                                     tagAGTATGTAGTGCATCGTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCTTTTTCATTATTTCACCTTAAAt   <  2:360795/139‑1 (MQ=255)
                                                                                                                      tGAGTATGTAGCGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCTTTTTCATTATTTCACCTTAAATa  >  1:240896/1‑141 (MQ=255)
                                                                                                                                 |                                                                                                                                 
ATAACCCGGATGAACGCCATCACAACCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGCGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCTTTTTCATTATTTCACCTTAAATA  >  USA300TCH1516_ALE/1643828‑1644086

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A