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 372,440 T→C 33.3% H1129H (CAT→CAC)  entF → enterobactin synthase multienzyme complex component, ATP‑dependent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE372,4400TC33.3% 54.8 / 37.6 72H1129H (CAT→CAC) entFenterobactin synthase multienzyme complex component, ATP‑dependent
Reads supporting (aligned to +/- strand):  ref base T (26/22);  new base C (16/8);  total (42/30)
Fisher's exact test for biased strand distribution p-value = 4.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.82e-01

CAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTCCCTTGGCGGTACGCTGGCGCAGGGT  >  minE/372372‑372491
                                                                    |                                                   
cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAGCAACCGCAt                                                     >  1:1907533/1‑69 (MQ=255)
cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                                     >  1:3166169/1‑69 (MQ=255)
cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                                     >  1:1475018/1‑69 (MQ=255)
cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                                     >  1:1486327/1‑69 (MQ=255)
cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                                     >  1:2208952/1‑69 (MQ=255)
cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                                     >  1:2481857/1‑69 (MQ=255)
cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                                     >  1:2888820/1‑69 (MQ=255)
cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                                     >  1:3031336/1‑69 (MQ=255)
cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                                     >  1:3143441/1‑69 (MQ=255)
cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                                     >  1:277768/1‑69 (MQ=255)
cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                                     >  1:3249783/1‑69 (MQ=255)
cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                                     >  1:358798/1‑69 (MQ=255)
cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                                     >  1:531600/1‑69 (MQ=255)
cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                                     >  1:796480/1‑69 (MQ=255)
cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                                     >  1:79649/1‑69 (MQ=255)
cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                                     >  1:99062/1‑69 (MQ=255)
cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                                     >  1:990802/1‑69 (MQ=255)
cAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCAt                                                     >  1:1383404/1‑69 (MQ=255)
   aCGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGc                                                  <  1:189660/69‑1 (MQ=255)
   aCGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGc                                                  <  1:97167/69‑1 (MQ=255)
       cggcAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCtt                                              <  1:529112/69‑1 (MQ=255)
       cggcAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCtt                                              <  1:2477982/69‑1 (MQ=255)
       cggcAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCtt                                              <  1:1069181/69‑1 (MQ=255)
           aaaCCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCttatta                                          <  1:1847800/69‑1 (MQ=255)
           aaaCCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCttatta                                          <  1:3423884/69‑1 (MQ=255)
                     gAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTgggg                                <  1:2634187/69‑1 (MQ=255)
                     gAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTgggg                                <  1:1972450/69‑1 (MQ=255)
                     gAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTgggg                                <  1:2205727/69‑1 (MQ=255)
                     gAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTgggg                                <  1:3349000/69‑1 (MQ=255)
                     gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                                    >  1:3254701/1‑65 (MQ=255)
                     gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                                    >  1:1100941/1‑65 (MQ=255)
                     gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                                    >  1:2690055/1‑65 (MQ=255)
                     gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                                    >  1:2208275/1‑65 (MQ=255)
                     gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                                    >  1:529773/1‑65 (MQ=255)
                     gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                                    >  1:1097823/1‑65 (MQ=255)
                     gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                                    >  1:3113843/1‑65 (MQ=255)
                     gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                                    >  1:1294558/1‑65 (MQ=255)
                     gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                                    >  1:583034/1‑65 (MQ=255)
                     gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                                    >  1:769735/1‑65 (MQ=255)
                     gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                                    >  1:840003/1‑65 (MQ=255)
                     gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                                    >  1:3213330/1‑65 (MQ=255)
                     gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                                    >  1:1806779/1‑65 (MQ=255)
                     gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                                    >  1:1660773/1‑65 (MQ=255)
                     gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                                    >  1:1532792/1‑65 (MQ=255)
                     gAAGTCTGCGAAGCGCATCTGGCAACCTTACTTGAACAACAACCGCACGGCCCATATTACctgct                                    >  1:1284053/1‑65 (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               <  1:3048020/69‑1 (MQ=255)
                                      tCTGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTCCCTTGGCGGTAc               <  1:293269/69‑1 (MQ=255)
                                      tCTGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTCCCTTGGCGGTAc               <  1:117501/69‑1 (MQ=255)
                                        tGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTCCCTTGGCGGTACGc             >  1:111651/1‑69 (MQ=255)
                                        tGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTCCCTTGGCGGTACGc             >  1:1460471/1‑69 (MQ=255)
                                        tGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTCCCTTGGCGGTACGc             >  1:751419/1‑69 (MQ=255)
                                        tGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTCCCTTGGCGGTACGc             >  1:2113597/1‑69 (MQ=255)
                                        tGGCAACCTTACTTGAACAACAACCGCACGGCCCatat                                            <  1:3372855/38‑1 (MQ=25)
                                        tGGCAACCTTACTTGAACAACAACCGCACGGCCCatat                                            <  1:343887/38‑1 (MQ=25)
                                        tGGCAACCTTACTTGAACAACAACCGCACGGCCCatat                                            <  1:542860/38‑1 (MQ=25)
                                        tGGCAACCTTACTTGAACAACAACCGCACGGCCCatat                                            <  1:850982/38‑1 (MQ=25)
                                        tGGCAACCTTACTTGAACAACAACCGCACGGCCCatat                                            <  1:1044338/38‑1 (MQ=25)
                                        tGGCAACCTTACTTGAACAACAACCGCACGGCCCatat                                            <  1:1870220/38‑1 (MQ=25)
                                        tGGCAACCTTACTTGAACAACAACCGCACGGCCCatat                                            <  1:2673422/38‑1 (MQ=25)
                                        tGGCAACCTTACTTGAACAACAACCGCACGGCCCatat                                            <  1:3099236/38‑1 (MQ=25)
                                          gCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           >  1:3175504/1‑53 (MQ=255)
                                          gCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           >  1:989472/1‑53 (MQ=255)
                                          gCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           >  1:1901464/1‑53 (MQ=255)
                                          gCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           >  1:2790243/1‑53 (MQ=255)
                                          gCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           >  1:1292728/1‑53 (MQ=255)
                                          gCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           >  1:3370508/1‑53 (MQ=255)
                                          gCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           >  1:2904687/1‑53 (MQ=255)
                                          gCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           >  1:1260134/1‑53 (MQ=255)
                                          gCAACGTTACTTGAACAAAAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           >  1:3056951/1‑53 (MQ=255)
                                          gCAACGTTAATTGAACAACAACCGCATGGCCCTTATTAc                                         >  1:1082974/1‑39 (MQ=255)
                                                  aCTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTCCCTTGGCGGTACGCTGGCGCAggg   <  1:1400537/69‑1 (MQ=255)
                                                    ttGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTCCCTTGGCGGTACGCTGGCGCAGGGt  <  1:3197962/68‑1 (MQ=255)
                                                      gAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           >  1:1442405/1‑41 (MQ=255)
                                                      gAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           >  1:1538793/1‑41 (MQ=255)
                                                      gAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           >  1:3164740/1‑41 (MQ=255)
                                                      gAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           <  1:1598536/41‑1 (MQ=255)
                                                      gAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           >  1:1089326/1‑41 (MQ=255)
                                                      gAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           >  1:2257210/1‑41 (MQ=255)
                                                      gAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           >  1:2404802/1‑41 (MQ=255)
                                                      gAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           <  1:2540721/41‑1 (MQ=255)
                                                      gAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           >  1:2566572/1‑41 (MQ=255)
                                                      gAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           >  1:2620021/1‑41 (MQ=255)
                                                      gAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           <  1:3131442/41‑1 (MQ=255)
                                                      gAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           >  1:1034948/1‑41 (MQ=255)
                                                      gAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           >  1:386230/1‑41 (MQ=255)
                                                      gAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTc                           >  1:2842887/1‑41 (MQ=255)
                                                                    |                                                   
CAGACGGCGGCAAACCTGGATGAAGTCTGCGAAGCGCATCTGGCAACGTTACTTGAACAACAACCGCATGGCCCTTATTACCTGCTGGGGTATTCCCTTGGCGGTACGCTGGCGCAGGGT  >  minE/372372‑372491

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