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 372,419 G→C 25.2% T1122T (ACG→ACC)  entF → enterobactin synthase multienzyme complex component, ATP‑dependent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE372,4190GC25.2% 155.6 / 53.3 99T1122T (ACG→ACC) entFenterobactin synthase multienzyme complex component, ATP‑dependent
Reads supporting (aligned to +/- strand):  ref base G (56/18);  new base C (17/8);  total (73/26)
Fisher's exact test for biased strand distribution p-value = 4.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.82e-01

AATGGCCCCATGCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTCCCTTGGCGGTACGC  >  minE/372360‑372480
                                                           |                                                             
aaTGGCCCCATGCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGa                                                       >  1:3355157/1‑68 (MQ=255)
    gCCCCATGCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGaacaac                                                  <  1:2212775/69‑1 (MQ=255)
          tGCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGc                                            >  1:2720023/1‑69 (MQ=255)
          tGCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGc                                            >  1:376769/1‑69 (MQ=255)
          tGCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGc                                            >  1:3002487/1‑69 (MQ=255)
           gCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGaac                                                     >  1:1755027/1‑59 (MQ=255)
           gCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCa                                           >  1:3005076/1‑69 (MQ=255)
           gCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCa                                           >  1:2294720/1‑69 (MQ=255)
           gCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCa                                           >  1:2208046/1‑69 (MQ=255)
           gCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCa                                           >  1:2321132/1‑69 (MQ=255)
           gCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCa                                           >  1:1977913/1‑69 (MQ=255)
           gCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCa                                           >  1:2728037/1‑69 (MQ=255)
           gCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCa                                           >  1:2732047/1‑69 (MQ=255)
           gCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCa                                           >  1:2949730/1‑69 (MQ=255)
           gCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCa                                           >  1:1724724/1‑69 (MQ=255)
           gCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCa                                           >  1:3165746/1‑69 (MQ=255)
           gCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCa                                           >  1:660780/1‑69 (MQ=255)
           gCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCa                                           >  1:3288251/1‑69 (MQ=255)
           gCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCa                                           >  1:3318361/1‑69 (MQ=255)
           gCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCa                                           >  1:1274096/1‑69 (MQ=255)
           gCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCa                                           >  1:1135770/1‑69 (MQ=255)
           gCAGACGGCGGCAAACCTGGATGAAGTCTGAGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCa                                           >  1:2024109/1‑69 (MQ=255)
            cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTg                                                        >  1:2760722/1‑55 (MQ=255)
            cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAGCAACCGCAt                                          >  1:1907533/1‑69 (MQ=255)
            cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCa                                           >  1:1154641/1‑68 (MQ=255)
            cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                          >  1:358798/1‑69 (MQ=255)
            cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                          >  1:99062/1‑69 (MQ=255)
            cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                          >  1:79649/1‑69 (MQ=255)
            cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                          >  1:796480/1‑69 (MQ=255)
            cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                          >  1:2481857/1‑69 (MQ=255)
            cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                          >  1:531600/1‑69 (MQ=255)
            cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                          >  1:3166169/1‑69 (MQ=255)
            cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                          >  1:277768/1‑69 (MQ=255)
            cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                          >  1:2888820/1‑69 (MQ=255)
            cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                          >  1:3249783/1‑69 (MQ=255)
            cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                          >  1:990802/1‑69 (MQ=255)
            cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                          >  1:3031336/1‑69 (MQ=255)
            cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                          >  1:3143441/1‑69 (MQ=255)
            cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                          >  1:1475018/1‑69 (MQ=255)
            cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                          >  1:1383404/1‑69 (MQ=255)
            cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                          >  1:1486327/1‑69 (MQ=255)
            cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                          >  1:2208952/1‑69 (MQ=255)
               aCGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGc                                       <  1:97167/69‑1 (MQ=255)
               aCGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGc                                       <  1:189660/69‑1 (MQ=255)
                   cggcAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCtt                                   <  1:529112/69‑1 (MQ=255)
                   cggcAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCtt                                   <  1:1069181/69‑1 (MQ=255)
                   cggcAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCtt                                   <  1:2477982/69‑1 (MQ=255)
                       aaaCCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCttatta                               <  1:3423884/69‑1 (MQ=255)
                       aaaCCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCttatta                               <  1:1847800/69‑1 (MQ=255)
                                 gAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTgggg                     <  1:1972450/69‑1 (MQ=255)
                                 gAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTgggg                     <  1:2634187/69‑1 (MQ=255)
                                 gAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTgggg                     <  1:3349000/69‑1 (MQ=255)
                                 gAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTgggg                     <  1:2205727/69‑1 (MQ=255)
                                 gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGaacaaca                                                 >  1:127925/1‑41 (MQ=255)
                                 gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                         >  1:3113843/1‑65 (MQ=255)
                                 gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                         >  1:583034/1‑65 (MQ=255)
                                 gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                         >  1:1097823/1‑65 (MQ=255)
                                 gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                         >  1:3213330/1‑65 (MQ=255)
                                 gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                         >  1:1294558/1‑65 (MQ=255)
                                 gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                         >  1:3254701/1‑65 (MQ=255)
                                 gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                         >  1:1100941/1‑65 (MQ=255)
                                 gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                         >  1:1284053/1‑65 (MQ=255)
                                 gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                         >  1:529773/1‑65 (MQ=255)
                                 gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                         >  1:769735/1‑65 (MQ=255)
                                 gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                         >  1:2208275/1‑65 (MQ=255)
                                 gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                         >  1:2690055/1‑65 (MQ=255)
                                 gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                         >  1:840003/1‑65 (MQ=255)
                                 gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                         >  1:1806779/1‑65 (MQ=255)
                                 gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                         >  1:1532792/1‑65 (MQ=255)
                                 gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                         >  1:1660773/1‑65 (MQ=255)
                                  aaGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTgggg                     <  1:3122691/68‑1 (MQ=255)
                                  aaGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGt                    >  1:2118446/1‑69 (MQ=255)
                                       tGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTcc               <  1:398995/69‑1 (MQ=255)
                                            aGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCGCtt                                   <  1:2995029/44‑1 (MQ=255)
                                                  tCTGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTCCCTTGGCGGTAc    <  1:293269/69‑1 (MQ=255)
                                                  tCTGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTCCCTTGGCGGTAc    <  1:3048020/69‑1 (MQ=255)
                                                  tCTGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTCCCTTGGCGGTAc    <  1:117501/69‑1 (MQ=255)
                                                    tGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTCCCTTGGCGGTACGc  >  1:751419/1‑69 (MQ=255)
                                                    tGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTCCCTTGGCGGTACGc  >  1:2113597/1‑69 (MQ=255)
                                                    tGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTCCCTTGGCGGTACGc  >  1:1460471/1‑69 (MQ=255)
                                                    tGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTCCCTTGGCGGTACGc  >  1:111651/1‑69 (MQ=255)
                                                    tGGCAACCTTACTTGAACAACAACCGCACGGCCCatat                                 <  1:850982/38‑1 (MQ=25)
                                                    tGGCAACCTTACTTGAACAACAACCGCACGGCCCatat                                 <  1:542860/38‑1 (MQ=25)
                                                    tGGCAACCTTACTTGAACAACAACCGCACGGCCCatat                                 <  1:1044338/38‑1 (MQ=25)
                                                    tGGCAACCTTACTTGAACAACAACCGCACGGCCCatat                                 <  1:343887/38‑1 (MQ=25)
                                                    tGGCAACCTTACTTGAACAACAACCGCACGGCCCatat                                 <  1:3372855/38‑1 (MQ=25)
                                                    tGGCAACCTTACTTGAACAACAACCGCACGGCCCatat                                 <  1:3099236/38‑1 (MQ=25)
                                                    tGGCAACCTTACTTGAACAACAACCGCACGGCCCatat                                 <  1:1870220/38‑1 (MQ=25)
                                                    tGGCAACCTTACTTGAACAACAACCGCACGGCCCatat                                 <  1:2673422/38‑1 (MQ=25)
                                                      gCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                >  1:1260134/1‑53 (MQ=255)
                                                      gCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                >  1:3370508/1‑53 (MQ=255)
                                                      gCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                >  1:1292728/1‑53 (MQ=255)
                                                      gCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                >  1:3175504/1‑53 (MQ=255)
                                                      gCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                >  1:2904687/1‑53 (MQ=255)
                                                      gCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                >  1:2790243/1‑53 (MQ=255)
                                                      gCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                >  1:989472/1‑53 (MQ=255)
                                                      gCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                >  1:1901464/1‑53 (MQ=255)
                                                      gCAACGTTACTTGAACAAAAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                >  1:3056951/1‑53 (MQ=255)
                                                      gCAACGTTAATTGAACAACAACCGCATGGCCCTTATTAc                              >  1:1082974/1‑39 (MQ=255)
                                                           |                                                             
AATGGCCCCATGCAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTCCCTTGGCGGTACGC  >  minE/372360‑372480

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A