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 2,732,551 T→C 40.4% D207D (GAT→GAC)  yheO → predicted DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,732,5510TC40.4% 36.4 / 67.3 94D207D (GAT→GAC) yheOpredicted DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (7/49);  new base C (29/9);  total (36/58)
Fisher's exact test for biased strand distribution p-value = 3.23e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01

AATAACGCCAAAAATCGTCAGATCGTGCTGAATCTCTACGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCTATCTCTACATCC  >  minE/2732486‑2732612
                                                                 |                                                             
aataaCGCCAAAAATCGTCAGATCGTGCTAAATCTCTACGAGAAAGGGATCTTCGATATTAAAGACGc                                                             <  1:478519/68‑1 (MQ=255)
aataaCGCCAAAAATCGTCAGATCGTGCTAAATCTCTACGAGAAAGGGATCTTCGATATTAAAGACGc                                                             <  1:1963998/68‑1 (MQ=255)
aataaCGCCAAAAATCGTCAGATCGTGCTAAATCTCTACGAGAAAGGGATCTTCGATATTAAAGACGc                                                             <  1:2096732/68‑1 (MQ=255)
aataaCGCCAAAAATCGTCAGATCGTGCTAAATCTCTACGAGAAAGGGATCTTCGATATTAAAGACGc                                                             <  1:2278200/68‑1 (MQ=255)
aataaCGCCAAAAATCGTCAGATCGTGCTAAATCTCTACGAGAAAGGGATCTTCGATATTAAAGACGc                                                             <  1:698909/68‑1 (MQ=255)
aataaCGCCAAAAATCGTCAGATCGTGCTAAATCTCTACGAGAAAGGGATCTTCGATATTAAAGACGc                                                             <  1:2713546/68‑1 (MQ=255)
aataaCGCCAAAAATCGTCAGATCGTGCTAAATCTCTACGAGAAAGGGATCTTCGATATTAAAGACGc                                                             <  1:2767352/68‑1 (MQ=255)
aataaCGCCAAAAATCGTCAGATCGTGCTAAATCTCTACGAGAAAGGGATCTTCGATATTAAAGACGc                                                             <  1:2781526/68‑1 (MQ=255)
aataaCGCCAAAAATCGTCAGATCGTGCTAAATCTCTACGAGAAAGGGATCTTCGATATTAAAGACGc                                                             <  1:3211013/68‑1 (MQ=255)
                gTCAGATCGTGCTGAATCTCTACGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTg                                            <  1:820149/69‑1 (MQ=255)
                        gTGCTGAATCTCTACGAGAAAGGGATCTTCGATATTAAAGATGCGATCGACCAGGTTGCTGACCGCCTg                                    <  1:3407222/69‑1 (MQ=255)
                        gTGCTGAATCTCTACGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTg                                    <  1:2917721/69‑1 (MQ=255)
                        gTGCTGAATCTCTACGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTg                                    <  1:1893256/69‑1 (MQ=255)
                        gTGCTGAATCTCTACGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTg                                    <  1:1966408/69‑1 (MQ=255)
                        gTGCTGAATCTCTACGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTg                                    <  1:1083846/69‑1 (MQ=255)
                        gTGCTGAATCTCTACGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTg                                    <  1:727929/69‑1 (MQ=255)
                        gTGCTGAATCTCTACGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTg                                    <  1:1096257/69‑1 (MQ=255)
                             gAATCTCTACGAGAAAGGGATCTTCGATATTAAGGATGCGATCAACCAGGTTGCTGACCGCCTGAACAt                               <  1:1621060/69‑1 (MQ=255)
                             gAATCTCTACGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACAt                               <  1:446465/69‑1 (MQ=255)
                             gAATCTCTACGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACAt                               <  1:201973/69‑1 (MQ=255)
                             gAATCTCTACGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACAt                               <  1:1983598/69‑1 (MQ=255)
                             gAATCTCTACGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACAt                               <  1:1969017/69‑1 (MQ=255)
                             gAATCTCTACGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACAt                               <  1:3357468/69‑1 (MQ=255)
                             gAATCTCTACGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACAt                               <  1:965772/69‑1 (MQ=255)
                             gAATCTCTACGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACAt                               <  1:3158694/69‑1 (MQ=255)
                             gAATCTCTACGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACAt                               <  1:1302904/69‑1 (MQ=255)
                             gAATCTCTACGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACAt                               <  1:1369039/69‑1 (MQ=255)
                             gAATCTCTACGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACAt                               <  1:881113/69‑1 (MQ=255)
                              aaTCTCTACGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACAt                               <  1:1336710/68‑1 (MQ=255)
                                      cGAGAAAGGGATCTTCGATATTAAAGATGCGATCa                                                        <  1:504418/35‑1 (MQ=255)
                                      cGAGAAAGGGATCTTCGATATTAAAGATGCGATCa                                                        <  1:3273364/35‑1 (MQ=255)
                                      cGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCaaa                        <  1:1790455/67‑1 (MQ=255)
                                      cGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCaaa                        <  1:2802495/67‑1 (MQ=255)
                                      cGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCaaa                        <  1:651100/67‑1 (MQ=255)
                                      cGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCaaa                        <  1:2353816/67‑1 (MQ=255)
                                              ggATGTTCGATATTAAAGACGCGATCAACCAGGTTGCTGAcc                                         >  1:2848612/1‑42 (MQ=37)
                                              ggATCTTCGATATTAAAGACGCGATCAACCATGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCt              >  1:3236168/1‑69 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGCCCGCCTGAACATCTCCAAACACACTGTCt              >  1:821583/1‑69 (MQ=39)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTg                                    >  1:1210933/1‑47 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCa                          >  1:215551/1‑57 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTc               >  1:751846/1‑68 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTc               >  1:2289738/1‑68 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTc               >  1:1440050/1‑68 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTc               >  1:2037682/1‑68 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCt              >  1:78832/1‑69 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCt              >  1:690871/1‑69 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCt              >  1:3000677/1‑69 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCt              >  1:691703/1‑69 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCt              >  1:1993319/1‑69 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCt              >  1:2866285/1‑69 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCt              >  1:1507857/1‑69 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCt              >  1:2817111/1‑69 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCt              >  1:150597/1‑69 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCt              >  1:3356860/1‑69 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCt              >  1:342761/1‑69 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCt              >  1:650425/1‑69 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCt              >  1:929463/1‑69 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCt              >  1:2637571/1‑69 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCt              >  1:1096521/1‑69 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCt              >  1:2205845/1‑69 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCt              >  1:2322305/1‑69 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCt              >  1:2250233/1‑69 (MQ=255)
                                              ggATCTTCGATATTAAAGACGCGATCAACCAGGTTGCTGACCGACTGAACATCTCCAAACACACTGTCt              >  1:1804494/1‑69 (MQ=39)
                                              ggATCTTCGATATTAAAGACGCGATAAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCt              >  1:656832/1‑69 (MQ=255)
                                               gATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCTa             >  1:1136251/1‑69 (MQ=255)
                                               gATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCTa             >  1:2867289/1‑69 (MQ=255)
                                               gATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCTa             >  1:1100777/1‑69 (MQ=255)
                                               gATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCTa             >  1:3403059/1‑69 (MQ=255)
                                               gATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCTa             >  1:2169134/1‑69 (MQ=255)
                                               gATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCTa             >  1:1832825/1‑69 (MQ=255)
                                               gATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTATCTa             >  1:261343/1‑69 (MQ=255)
                                                     cGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCTAtctc         <  1:1320541/67‑1 (MQ=255)
                                                       atatTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCTAtctc         <  1:278538/65‑1 (MQ=255)
                                                       atatTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCTAtctc         <  1:269694/65‑1 (MQ=255)
                                                       atatTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCTAtctc         <  1:948711/65‑1 (MQ=255)
                                                        tatTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCTAtctc         <  1:3314040/64‑1 (MQ=255)
                                                        tatTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCTATCTCTACa     <  1:1050611/68‑1 (MQ=255)
                                                        tatTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCTATCTCTACa     <  1:31791/68‑1 (MQ=255)
                                                        tatTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCTATCTCTACa     <  1:3006951/68‑1 (MQ=255)
                                                        tatTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCTATCTCTACa     <  1:1077773/68‑1 (MQ=255)
                                                        tatTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCTATCTCTACa     <  1:2350956/68‑1 (MQ=255)
                                                          ttAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTc               <  1:2280413/56‑1 (MQ=255)
                                                          ttAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTc               <  1:978495/56‑1 (MQ=255)
                                                          ttAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTc               <  1:1019654/56‑1 (MQ=255)
                                                          ttAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTc               <  1:1416290/56‑1 (MQ=255)
                                                          ttAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTc               <  1:1449891/56‑1 (MQ=255)
                                                          ttAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTc               <  1:1576679/56‑1 (MQ=255)
                                                          ttAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTc               <  1:1752057/56‑1 (MQ=255)
                                                          ttAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTc               <  1:2233745/56‑1 (MQ=255)
                                                          ttAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTc               <  1:2650828/56‑1 (MQ=255)
                                                          ttAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTc               <  1:2874198/56‑1 (MQ=255)
                                                          ttAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTc               <  1:3278620/56‑1 (MQ=255)
                                                          ttAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCTATCTCTACATcc  <  1:527713/69‑1 (MQ=255)
                                                          ttAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCTATCTCTACATcc  <  1:3360617/69‑1 (MQ=255)
                                                                 |                                                             
AATAACGCCAAAAATCGTCAGATCGTGCTGAATCTCTACGAGAAAGGGATCTTCGATATTAAAGATGCGATCAACCAGGTTGCTGACCGCCTGAACATCTCCAAACACACTGTCTATCTCTACATCC  >  minE/2732486‑2732612

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