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 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,713,305 A→G 39.8% S352S (AGT→AGC)  nirB ← nitrite reductase, large subunit, NAD(P)H‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,713,3050AG39.8% 53.7 / 87.4 123S352S (AGT→AGC) nirBnitrite reductase, large subunit, NAD(P)H‑binding
Reads supporting (aligned to +/- strand):  ref base A (40/34);  new base G (16/33);  total (56/67)
Fisher's exact test for biased strand distribution p-value = 2.64e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 123 total aligned reads displayed.

TACCGCACCGAGCAGGGTTTTGTTGTCTTCGCTGACAATCAGGCGTTTGTAGATCTCTTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCACCAAT  >  minE/2713245‑2713364
                                                            |                                                           
tACCGCACCTAGCAGGGTTTTGTTGTCTTCGCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtcgtc                                                     <  1:3176591/69‑1 (MQ=255)
tACCGCACCGAGCAGGGTTTTGTTGTCTTCGCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtcgtc                                                     <  1:2583422/69‑1 (MQ=255)
tACCGCACCGAGCAGGGTTTTGTTGTCTTCGCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtcgtc                                                     <  1:334882/69‑1 (MQ=255)
tACCGCACCGAGCAGGGTTTTGTTGTCTTCGCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtcgtc                                                     <  1:1473426/69‑1 (MQ=255)
tACCGCACCGAGCAGGGTTTTGTTGTCTTCGCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtcgtc                                                     <  1:511530/69‑1 (MQ=255)
tACCGCACCGAGCAGGGTTTTGTTGTCTTCGCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtcgtc                                                     <  1:1315535/69‑1 (MQ=255)
tACCGCACCGAGCAGGGTTTTGTTGTCTTCGCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtcgtc                                                     <  1:706434/69‑1 (MQ=255)
tACCGCACCGAGCAGGGTTTTGTTGTCTTCGCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtcgtc                                                     <  1:2941060/69‑1 (MQ=255)
tACCGCACCGAGCAGGGTTTTGTTGTCTTCGCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtcgtc                                                     <  1:2884222/69‑1 (MQ=255)
tACCGCACCGAGCAGGGTTTTGTTGTCTTCGCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtcgtc                                                     <  1:2413534/69‑1 (MQ=255)
tACCGCACCGAGCAGGGTTTTGTTGTCTTCGCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtcgtc                                                     <  1:2769/69‑1 (MQ=255)
tACCGCACCGAGCAGGGTTTTGTTGTCTTCGCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtagtc                                                     <  1:1686914/69‑1 (MQ=255)
              gggTTTTGTTGTCTTCGCTGACAATCAGGCGTTTGTAGATCTCTTTACTTTCGTCGAGGTAAACGTAGc                                       <  1:2963509/69‑1 (MQ=255)
                gTTTTGTTGTCTTCGCTGACAATCAGGCGTTTGTAGATCTCTTTACTTTCGTCGAGGTAAACGTAGCTa                                     >  1:1914954/1‑69 (MQ=255)
                gTTTTGTTGTCTTCGCTGACAATCAGGCGTTTGTAGATCTCTTTACTTTCGTCGAGGTAAACGTAGCTa                                     >  1:1790279/1‑69 (MQ=255)
                gTTTTGTTGTCTTCGCTGACAATCAGGCGTTTGTAGATCTCTTTACTTTCGTCGAGGTAAACGTAGCTa                                     >  1:1681068/1‑69 (MQ=255)
                gTTTTGTTGTCTTCGCTGACAATCAGGCGTTTGTAGATCTCTTTACTTTCGTCGAGGTAAACGTAGCTa                                     >  1:3276538/1‑69 (MQ=255)
                gTTTTGTTGTCTTCGCTGACAATCAGGCGTTTGTAGATCTCTTTACTTTCGTCGAGGTAAACGTAGCTa                                     >  1:1644495/1‑69 (MQ=255)
                gTTTTGTTGTCTTCGCTGACAATCAGGCGTTTGTAGATCTCTTTACTTTCGTCGAGGTAAACGTAGCTa                                     >  1:1430882/1‑69 (MQ=255)
                gTTTTGTTGTCTTCGCTGACAATCAGGCGTTTGTAGATCTCTTTACTTTCGTCGAGGTAAACGTAGCTa                                     >  1:624657/1‑69 (MQ=255)
                             cGCTGACAATCAGGCGTTTGTAGATCTCTTTGCttt                                                         >  1:3106066/1‑36 (MQ=255)
                             cGCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtcg                                                       >  1:2016789/1‑38 (MQ=255)
                             cGCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtcg                                                       >  1:1040918/1‑38 (MQ=255)
                             cGCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtcg                                                       >  1:928845/1‑38 (MQ=255)
                             cGCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtcg                                                       >  1:1169520/1‑38 (MQ=255)
                             cGCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtcg                                                       >  1:2148949/1‑38 (MQ=255)
                             cGCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtcg                                                       >  1:83643/1‑38 (MQ=255)
                             cGCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtcg                                                       >  1:711/1‑38 (MQ=255)
                             cGCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtcg                                                       >  1:45835/1‑38 (MQ=255)
                             cGCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtcg                                                       >  1:1926386/1‑38 (MQ=255)
                             cGCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtc                                                        >  1:147544/1‑37 (MQ=255)
                             agCTGACAATCAGGCGTTTGTAGATCTCTTTGCTTtcg                                                       >  1:3070737/2‑38 (MQ=38)
                                       cAGGCGTTTGTAGATCTCTTTACTTTCGTCGAGGTAAACGTAGCt                                      >  1:3033841/1‑45 (MQ=255)
                                       cAGGCGTTTGTAGATCTCTTTACTTTCGTCGAGGTAAACGTAGCt                                      >  1:3028233/1‑45 (MQ=255)
                                       cAGGCGTTTGTAGATCTCTTTACTTTCGTCGAGGTAAACGTAGCt                                      >  1:692783/1‑45 (MQ=255)
                                       cAGGCGTTTGTAGATCTCTTTACTTTCGTCGAGGTAAACGTAGCt                                      >  1:2077954/1‑45 (MQ=255)
                                       cAGGCGTTTGTAGATCTCTTTACTTTCGTCGAGGTAAACGTAGCt                                      >  1:680401/1‑45 (MQ=255)
                                       cAGGCGTTTGTAGATCTCTTTACTTTCGTCGAGGTAAACGTAGCt                                      >  1:2344028/1‑45 (MQ=255)
                                       cAGGCGTTTGTAGATCTCTTTACTTTCGTCGAGGTAAACGTAGCt                                      >  1:2794580/1‑45 (MQ=255)
                                       cAGGCGTTTGTAGATCTCTTTACTTTCGTCGAGGTAAACGTAGCt                                      >  1:1439514/1‑45 (MQ=255)
                                       cAGGCGTTTGTAGATCTCTTTACTTTCGTCGAGGTAAACGTAGCt                                      >  1:260918/1‑45 (MQ=255)
                                       cAGGCGTTTGTAGATCTCTTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTg              >  1:2896802/1‑69 (MQ=255)
                                             tttGTAGATCTCTTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTTCGACCGTGCGCATc        >  1:1164788/1‑69 (MQ=255)
                                             tttGTAGATCTCTTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATc        >  1:2723466/1‑69 (MQ=255)
                                                   gATCTCTTTGCTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGc                         <  1:2526046/46‑1 (MQ=255)
                                                   gATCTCTTTGCTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGc                         <  1:369406/46‑1 (MQ=255)
                                                   gATCTCTTTGCTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGc                         <  1:1459985/46‑1 (MQ=255)
                                                   gATCTCTTTGCTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGc                         <  1:1398521/46‑1 (MQ=255)
                                                   gATCTCTTTGCTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGc                         <  1:1594917/46‑1 (MQ=255)
                                                   gATCTCTTTGCTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGc                         <  1:3238479/46‑1 (MQ=255)
                                                   gATCTCTTTGCTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGc                         <  1:3216585/46‑1 (MQ=255)
                                                   gATCTCTTTGCTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGc                         <  1:3211054/46‑1 (MQ=255)
                                                   gATCTCTTTGCTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGc                         <  1:699787/46‑1 (MQ=255)
                                                   gATCTCTTTGCTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGc                         <  1:3132907/46‑1 (MQ=255)
                                                   gATCTCTTTGCTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGc                         <  1:1615433/46‑1 (MQ=255)
                                                   gATCTCTTTGCTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGc                         <  1:1678918/46‑1 (MQ=255)
                                                   gATCTCTTTGCTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGc                         <  1:2984178/46‑1 (MQ=255)
                                                   gATCTCTTTGCTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGc                         <  1:2568312/46‑1 (MQ=255)
                                                   gATCTCTTTGCTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGc                         <  1:2397076/46‑1 (MQ=255)
                                                   gATCTCTTTGCTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGc                         <  1:2387467/46‑1 (MQ=255)
                                                   gATCTCTTTGCTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGc                         <  1:1231011/46‑1 (MQ=255)
                                                   gATCTCTTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCACCaa   <  1:3405465/68‑1 (MQ=255)
                                                   gATCTCTTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCACCAAt  <  1:3036929/69‑1 (MQ=255)
                                                   gATCTCTTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCACCAAt  <  1:1961247/69‑1 (MQ=255)
                                                   gATCTCTTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCACCAAt  <  1:1234725/69‑1 (MQ=255)
                                                   gATCTCTTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCACCAAt  <  1:711634/69‑1 (MQ=255)
                                                   gATCTCTTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCACCAAt  <  1:3184891/69‑1 (MQ=255)
                                                   gATCTCTTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCACCAAt  <  1:246647/69‑1 (MQ=255)
                                                   gATCTCTTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCACCAAt  <  1:899306/69‑1 (MQ=255)
                                                   gATCTCTTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCACCAAt  <  1:411955/69‑1 (MQ=255)
                                                   gATCTCTTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCACCAAt  <  1:1418820/69‑1 (MQ=255)
                                                    aTCTCTTTGCTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGc                         <  1:1320499/45‑1 (MQ=255)
                                                      ctctTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCACCAAt  <  1:412434/66‑1 (MQ=255)
                                                      ctctTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCACCAAt  <  1:43852/66‑1 (MQ=255)
                                                      ctctTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCACCAAt  <  1:919553/66‑1 (MQ=255)
                                                      ctctTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCACCAAt  <  1:1062221/66‑1 (MQ=255)
                                                      ctctTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCACCAAt  <  1:2656034/66‑1 (MQ=255)
                                                      ctctTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCACCAAt  <  1:2106459/66‑1 (MQ=255)
                                                      ctctTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCACCAAt  <  1:2192490/66‑1 (MQ=255)
                                                      ctctTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCACCAAt  <  1:2034365/66‑1 (MQ=255)
                                                          ttACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCAcc     >  1:684155/1‑59 (MQ=255)
                                                          ttACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCAcc     >  1:489183/1‑59 (MQ=255)
                                                          ttACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCAcc     >  1:986777/1‑59 (MQ=255)
                                                          ttACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCAcc     >  1:3434697/1‑59 (MQ=255)
                                                          ttACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCAcc     >  1:3432442/1‑59 (MQ=255)
                                                          ttACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCAcc     >  1:3430965/1‑59 (MQ=255)
                                                          ttACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCAcc     >  1:3393991/1‑59 (MQ=255)
                                                          ttACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCAcc     >  1:1583247/1‑59 (MQ=255)
                                                          ttACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCAcc     >  1:2481610/1‑59 (MQ=255)
                                                          ttACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCAcc     >  1:1597078/1‑59 (MQ=255)
                                                          ttACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCAcc     >  1:1013790/1‑59 (MQ=255)
                                                          ttACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCAcc     >  1:2911051/1‑59 (MQ=255)
                                                          ttACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCAc      >  1:1963515/1‑58 (MQ=255)
                                                          ttACTTTAGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCAcc     >  1:2692671/1‑59 (MQ=255)
                                                           tACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTgcg            <  1:1232995/51‑1 (MQ=255)
                                                           tACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTgcg            <  1:805390/51‑1 (MQ=255)
                                                           tACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTgcg            <  1:2890043/51‑1 (MQ=255)
                                                           tACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTgcg            <  1:1522112/51‑1 (MQ=255)
                                                           tACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTgcg            <  1:3335240/51‑1 (MQ=255)
                                                           tACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTgcg            <  1:2602336/51‑1 (MQ=255)
                                                            |                                                           
TACCGCACCGAGCAGGGTTTTGTTGTCTTCGCTGACAATCAGGCGTTTGTAGATCTCTTTACTTTCGTCGAGGTAAACGTAGCTACGTGCGCCAGGCGTGCGACCGTGCGCATCACCAAT  >  minE/2713245‑2713364

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A