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 1,632,211 C→T 42.2% R71R (CGC→CGT)  narQ → sensory histidine kinase in two‑component regulatory system with NarP (NarL)

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,632,2110CT42.2% 44.8 / 87.1 119R71R (CGC→CGT) narQsensory histidine kinase in two‑component regulatory system with NarP (NarL)
Reads supporting (aligned to +/- strand):  ref base C (20/48);  new base T (25/25);  total (45/74)
Fisher's exact test for biased strand distribution p-value = 3.44e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.14e-01

Only 100 of 119 total aligned reads displayed.

TATGCAGAGTTACCGCCTGGGCTACGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACGTCTGGTATGTGCCAGA  >  minE/1632148‑1632276
                                                               |                                                                 
tATGCAGAGTTACCGCCTGGGCTACGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGt                                                               <  1:1021479/68‑1 (MQ=255)
tATGCAGAGTTACCGCCTGGGCTACGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGt                                                               <  1:704234/68‑1 (MQ=255)
tATGCAGAGTTACCGCCTGGGCTACGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGt                                                               <  1:299563/68‑1 (MQ=255)
tATGCAGAGTTACCGCCTGGGCTACGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGt                                                               <  1:2969316/68‑1 (MQ=255)
tATGCAGAGTTACCGCCTGGGCTACGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGt                                                               <  1:2854063/68‑1 (MQ=255)
tATGCAGAGTTACCGCCTGGGCTACGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGt                                                               <  1:2792352/68‑1 (MQ=255)
tATGCAGAGTTACCGCCTGGGCTACGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGt                                                               <  1:2095904/68‑1 (MQ=255)
tATGCAGAGTTACCGCCTGGGCTACGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGt                                                               <  1:1181673/68‑1 (MQ=255)
tATGCAGAGTTACCGCCTGGGCTACGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGACAGt                                                               <  1:1165085/68‑1 (MQ=255)
 aTGCAGAGTTACCGCCTGGGCTACGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGt                                                               <  1:2633393/67‑1 (MQ=255)
           aCCGCCTGGGCTACGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGTTa                                                             >  1:2515637/1‑59 (MQ=255)
           aCCGCCTGGGCTACGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGTTAt                                                            >  1:11291/1‑60 (MQ=255)
           aCCGCCTGGGCTACGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGTTAt                                                            >  1:2927260/1‑60 (MQ=255)
           aCCGCCTGGGCTACGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGTTAt                                                            >  1:3020069/1‑60 (MQ=255)
                 tGGGCTACGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGc                                             <  1:127287/69‑1 (MQ=255)
                 tGGGCTACGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGc                                             <  1:74694/69‑1 (MQ=255)
                 tGGGCTACGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGc                                             <  1:1443832/69‑1 (MQ=255)
                 tGGGCTACGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGc                                             <  1:349484/69‑1 (MQ=255)
                       aCGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCAc                                       <  1:2084381/69‑1 (MQ=255)
                       aCGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCAc                                       <  1:945677/69‑1 (MQ=255)
                       aCGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCAc                                       <  1:2533661/69‑1 (MQ=255)
                       aCGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCAc                                       <  1:1122125/69‑1 (MQ=255)
                       aCGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCAc                                       <  1:2886664/69‑1 (MQ=255)
                       aCGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCAc                                       <  1:1044625/69‑1 (MQ=255)
                       aCGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCAc                                       <  1:3234239/69‑1 (MQ=255)
                       aCGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCAc                                       <  1:458494/69‑1 (MQ=255)
                       aCGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCAc                                       <  1:533029/69‑1 (MQ=255)
                       aCGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCAc                                       <  1:543678/69‑1 (MQ=255)
                       aCGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCAc                                       <  1:1024874/69‑1 (MQ=255)
                       aCGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCAc                                       <  1:883572/69‑1 (MQ=255)
                       aCGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCAc                                       <  1:916048/69‑1 (MQ=255)
                       aCGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCAc                                       <  1:1137258/69‑1 (MQ=255)
                       aCGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCAc                                       <  1:1186342/69‑1 (MQ=255)
                       aCGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCAc                                       <  1:1419423/69‑1 (MQ=255)
                       aCGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCAc                                       <  1:1435679/69‑1 (MQ=255)
                       aCGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCAc                                       <  1:1373842/69‑1 (MQ=255)
                       aCGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGAAGGCACTGCATTCAc                                       <  1:2790649/69‑1 (MQ=255)
                       aCGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCATCAGTTATTTCAGCAGGCACTGCATTCAc                                       <  1:3045159/69‑1 (MQ=255)
                        cGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGt                                                               <  1:1903160/44‑1 (MQ=255)
                         gACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCTGt                                                               <  1:1119351/43‑1 (MQ=255)
                          aCTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCgg                                    <  1:2975749/69‑1 (MQ=255)
                          aCTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCgg                                    <  1:3316019/69‑1 (MQ=255)
                          aCTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCgg                                    <  1:3432586/69‑1 (MQ=255)
                          aCTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCgg                                    <  1:2292876/69‑1 (MQ=255)
                          aCTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCgg                                    <  1:741735/69‑1 (MQ=255)
                          aCTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCgg                                    <  1:2572703/69‑1 (MQ=255)
                           cTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCgg                                    <  1:3278526/68‑1 (MQ=255)
                                   gTGGCAGTCCACAACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaacca                           <  1:1982432/69‑1 (MQ=255)
                                   gTGGCAGTCCACAACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaacca                           <  1:2417126/69‑1 (MQ=255)
                                   gTGGCAGTCCACAACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaacca                           <  1:2701171/69‑1 (MQ=255)
                                   gTGGCAGTCCACAACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaacca                           <  1:1669478/69‑1 (MQ=255)
                                       cAGTCGACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCAc                                       >  1:1797805/1‑53 (MQ=255)
                                       cAGTCCACAACTCAATTCACATCGTCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaaccaatc                        >  1:2239929/1‑66 (MQ=255)
                                       cAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCAtt                                          >  1:1859130/1‑50 (MQ=255)
                                       cAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaaccaatc                        >  1:3008941/1‑66 (MQ=255)
                                       cAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaaccaatc                        >  1:3162079/1‑66 (MQ=255)
                                       cAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaaccaatc                        >  1:565580/1‑66 (MQ=255)
                                       cAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaaccaatc                        >  1:3308696/1‑66 (MQ=255)
                                       cAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaaccaatc                        >  1:3413033/1‑66 (MQ=255)
                                       cAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaaccaatc                        >  1:3206234/1‑66 (MQ=255)
                                       cAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaaccaatc                        >  1:368220/1‑66 (MQ=255)
                                       cAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaaccaatc                        >  1:3263966/1‑66 (MQ=255)
                                       cAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaaccaatc                        >  1:1069307/1‑66 (MQ=255)
                                       cAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaaccaatc                        >  1:2088725/1‑66 (MQ=255)
                                       cAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaaccaatc                        >  1:9358/1‑66 (MQ=255)
                                       cAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaaccaatc                        >  1:907070/1‑66 (MQ=255)
                                       cAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaaccaatc                        >  1:23028/1‑66 (MQ=255)
                                       cAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaaccaatc                        >  1:2340904/1‑66 (MQ=255)
                                       cAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaaccaatc                        >  1:1302202/1‑66 (MQ=255)
                                       cAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaaccaatc                        >  1:2496267/1‑66 (MQ=255)
                                       cAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaaccaatc                        >  1:2657647/1‑66 (MQ=255)
                                       cAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaaccaatc                        >  1:2674891/1‑66 (MQ=255)
                                       cAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaaccaatc                        >  1:657754/1‑66 (MQ=255)
                                       cAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaaccaatc                        >  1:2934377/1‑66 (MQ=255)
                                       cAGTCCACAACTCAATGCACATCGTCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaaccaat                         >  1:1020463/1‑66 (MQ=255)
                                         gTCCACAACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTaacca                           <  1:112227/63‑1 (MQ=255)
                                            cacaACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAAc                   >  1:2973096/1‑68 (MQ=255)
                                            cacaACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACg                  >  1:44650/1‑69 (MQ=255)
                                            cacaACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACg                  >  1:586450/1‑69 (MQ=255)
                                            cacaACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACg                  >  1:2031981/1‑69 (MQ=255)
                                            cacaACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACg                  >  1:1675791/1‑69 (MQ=255)
                                            cacaACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACg                  >  1:3210643/1‑69 (MQ=255)
                                            cacaACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACg                  >  1:2734796/1‑69 (MQ=255)
                                            cacaACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACg                  >  1:3052595/1‑69 (MQ=255)
                                            cacaACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACg                  >  1:3266261/1‑69 (MQ=255)
                                               aaCTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACg                  <  1:1888809/66‑1 (MQ=255)
                                               aaCTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACg                  >  1:234307/1‑66 (MQ=255)
                                               aaCTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACg                  <  1:744245/66‑1 (MQ=255)
                                               aaCTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACg                  <  1:581866/66‑1 (MQ=255)
                                               aaCTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACg                  <  1:173775/66‑1 (MQ=255)
                                               aaCTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACg                  <  1:1468098/66‑1 (MQ=255)
                                                aCTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACg                  <  1:2449423/65‑1 (MQ=255)
                                                 cTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAATGTCTgg             <  1:1478077/69‑1 (MQ=255)
                                                 cTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACGTCTgg             <  1:1747405/69‑1 (MQ=255)
                                                 cTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACGTCTgg             <  1:1245715/69‑1 (MQ=255)
                                                 cTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACGTCTgg             <  1:2053253/69‑1 (MQ=255)
                                                  tCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACg                  <  1:3183604/63‑1 (MQ=255)
                                                      tGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACGTCTGGTAtg         <  1:2115759/68‑1 (MQ=255)
                                                        cacaTCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACGTCTGGTAtgt        >  1:2228248/1‑67 (MQ=255)
                                                              gCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACGTCTGGTATGTGCCAGa  >  1:2605387/1‑67 (MQ=255)
                                                               |                                                                 
TATGCAGAGTTACCGCCTGGGCTACGACTTGCAAAGTGGCAGTCCACAACTCAATGCACATCGCCAGTTATTTCAGCAGGCACTGCATTCACCGGTATTAACCAACCTCAACGTCTGGTATGTGCCAGA  >  minE/1632148‑1632276

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A