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 2,902,635 G→C 28.1% L470L (CTC→CTG)  nrdD ← anaerobic ribonucleoside‑triphosphate reductase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,902,6350GC28.1% 97.5 / 41.4 71L470L (CTC→CTG) nrdDanaerobic ribonucleoside‑triphosphate reductase
Reads supporting (aligned to +/- strand):  ref base G (20/31);  new base C (12/8);  total (32/39)
Fisher's exact test for biased strand distribution p-value = 1.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01

TAACCCAGCGAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCACCTTCCATATAGAGGATCGGGGCCACGCGCGCTTTCACGCCTTCGAGACG  >  minE/2902573‑2902703
                                                              |                                                                    
tAACCCAGCGAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGacgc                                                                >  1:2354542/1‑69 (MQ=255)
tAACCCAGCGAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGacgc                                                                >  1:3108634/1‑69 (MQ=255)
tAACCCAGCGAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGacg                                                                 >  1:2730867/1‑68 (MQ=255)
       gCGAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACTCACGCcac                                                         <  1:2769164/69‑1 (MQ=255)
       gCGAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcac                                                         <  1:2328591/69‑1 (MQ=255)
       gCGAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcac                                                         <  1:188325/69‑1 (MQ=255)
       gCGAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcac                                                         <  1:1098645/69‑1 (MQ=255)
       gCGAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcac                                                         <  1:597067/69‑1 (MQ=255)
       gCGAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcac                                                         <  1:508800/69‑1 (MQ=255)
         gAAATAGACGCACGACTGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcaca                                                        >  1:2296278/1‑68 (MQ=255)
         gAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcaca                                                        >  1:1937821/1‑68 (MQ=255)
         gAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcaca                                                        >  1:1922111/1‑68 (MQ=255)
         gAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcaca                                                        >  1:2817401/1‑68 (MQ=255)
         gAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcaca                                                        >  1:3064935/1‑68 (MQ=255)
         gAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcaca                                                        >  1:474307/1‑68 (MQ=255)
         gAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcaca                                                        >  1:2413330/1‑68 (MQ=255)
         gAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcaca                                                        >  1:1287307/1‑68 (MQ=255)
         gAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATAGAGACGCACGCcac                                                         >  1:2167549/1‑67 (MQ=255)
           aaTAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGc                                                     <  1:784270/69‑1 (MQ=255)
            aTAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCa                                                    <  1:356284/69‑1 (MQ=255)
            aTAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCa                                                    <  1:1438916/69‑1 (MQ=255)
            aTAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCa                                                    <  1:703003/69‑1 (MQ=255)
            aTAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCa                                                    <  1:2708224/69‑1 (MQ=255)
            aTAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCa                                                    <  1:984427/69‑1 (MQ=255)
             tAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCa                                                    <  1:2144843/68‑1 (MQ=255)
             tAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCa                                                    <  1:206935/68‑1 (MQ=255)
                 cGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCACCTTc                                               <  1:1723993/69‑1 (MQ=255)
                  gCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCACCTTc                                               <  1:2848847/68‑1 (MQ=255)
                         cGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTga                                                                     <  1:176952/39‑1 (MQ=255)
                             tttGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCACCTTCCa                                             >  1:915212/1‑59 (MQ=255)
                             tttGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCACCTTCCa                                             >  1:1224992/1‑59 (MQ=255)
                                gAAGATTTCAGAAACGTCGTCGTCAGTATTCAGACGCACGCCACAAGCGCCTTCCATATAGAGGATCg                                 <  1:733500/68‑1 (MQ=255)
                                gAAGATTTCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGCGCCTTCCATATAGAGGATCg                                 <  1:2553805/68‑1 (MQ=255)
                                gAAGATTTCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGCGCCTTCCATATAGAGGATCg                                 <  1:2465496/68‑1 (MQ=255)
                                gAAGATTTCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGCGCCTTCCATATAGAGGATCg                                 <  1:294318/68‑1 (MQ=255)
                                gAAGATTTCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGCGCCTTCCATATAGAGGATCg                                 <  1:737630/68‑1 (MQ=255)
                                gAAGATTTCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGCGCCTTCCATATAGAGGATCg                                 <  1:992176/68‑1 (MQ=255)
                                gAAGATTTCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGCGCCTTCCATATAGAGGATCg                                 <  1:1634957/68‑1 (MQ=255)
                                gAAGATTTCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGCGCCTTCCATATAGAGGATCg                                 <  1:2056036/68‑1 (MQ=255)
                                   gATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAACCACCTTCCATATAGAGGATCGGGGc                             <  1:1213623/69‑1 (MQ=255)
                                      ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg                                                    >  1:3067725/1‑42 (MQ=37)
                                      ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg                                                    >  1:3136689/1‑42 (MQ=37)
                                      ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg                                                    >  1:3144642/1‑42 (MQ=37)
                                      ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg                                                    >  1:3301833/1‑42 (MQ=37)
                                      ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg                                                    >  1:1573642/1‑42 (MQ=37)
                                      ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg                                                    >  1:1546488/1‑42 (MQ=37)
                                      ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg                                                    >  1:2753276/1‑42 (MQ=37)
                                      ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg                                                    >  1:1458954/1‑42 (MQ=37)
                                      ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg                                                    >  1:1402142/1‑42 (MQ=37)
                                      ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg                                                    >  1:2600264/1‑42 (MQ=37)
                                      ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg                                                    >  1:1370261/1‑42 (MQ=37)
                                      ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg                                                    >  1:741693/1‑42 (MQ=37)
                                                  atcGTCAGCATTGAGACGCACGCCACAAGCACCTTCCata                                           >  1:373009/1‑40 (MQ=255)
                                                  atcGTCAGCATTGAGACGCACGCCACAAGCACCTTCCata                                           >  1:1396698/1‑40 (MQ=255)
                                                  atcGTCAGCATTGAGACGCACGCCACAAGCACCTTCCata                                           >  1:21579/1‑40 (MQ=255)
                                                  atcGTCAGCATTGAGACGCACGCCACAAGCACCTTCCata                                           >  1:1634319/1‑40 (MQ=255)
                                                  atcGTCAGCATTGAGACGCACGCCACAAGCACCTTCCata                                           >  1:1812196/1‑40 (MQ=255)
                                                  atcGTCAGCATTGAGACGCACGCCACAAGCACCTTCCata                                           >  1:1718410/1‑40 (MQ=255)
                                                    cGTCAGCATTGAGACGCACGCCACAAGCACCTTCCATATAGAgg                                     <  1:1665692/44‑1 (MQ=255)
                                                    cGTCAGCATTGAGACGCACGCCACAAGCACCTTCCATATAGAgg                                     <  1:125064/44‑1 (MQ=255)
                                                    cGTCAGCATTGAGACGCACGCCACAAGCACCTTCCATATAGAgg                                     <  1:2435310/44‑1 (MQ=255)
                                                    cGTCAGCATTGAGACGCACGCCACAAGCACCTTCCATATAGAgg                                     <  1:1962856/44‑1 (MQ=255)
                                                    cGTCAGCATTGAGACGCACGCCACAAGCACCTTCCATATAGAgg                                     <  1:640396/44‑1 (MQ=255)
                                                    cGTCAGCATTGAGACGCACGCCACAAGCACCTTCCATATAGAgg                                     <  1:1412116/44‑1 (MQ=255)
                                                    cGTCAGCATTGAGACGCACGCCACAAGCACCTTCCATATAGAgg                                     <  1:443872/44‑1 (MQ=255)
                                                    cGTCAGCATTGAGACGCACGCCACAAGCACCTTCCATATAGAgg                                     <  1:2883111/44‑1 (MQ=255)
                                                    cGTCAGCATTGAGACGCACGCCACAAGCACCTTCCATATAGAgg                                     <  1:3362520/44‑1 (MQ=255)
                                                    cGTCAGCATTGAGACGCACGCCACAAGCACCTTCCATATAGAgg                                     <  1:332109/44‑1 (MQ=255)
                                                    cGTCAGCATTGAGACGCACGCCACAAGCACCTTCCATATAGAgg                                     <  1:319448/44‑1 (MQ=255)
                                                    cGTCAGCATTGAGACGCACGCCACAAGAACCTTCCATATAGAgg                                     <  1:800899/44‑1 (MQ=255)
                                                    cGTCAGCATTGAGACGCACCCCACAAGCACCTTCCATATAGAgg                                     <  1:1746492/44‑1 (MQ=255)
                                                             tGAGACGCACGCCACAAGCACCTTCCATATAGAGGATCGGGGCCACGCGCGCTTTCACGCCTTCGAGAc   <  1:1677196/69‑1 (MQ=255)
                                                              gagaCGCACGCCACAAGCACCTTCCATATAGAGGATCGGGGCCACGCGCGCTTTCACGCCTTCGAGACg  >  1:2875332/1‑69 (MQ=255)
                                                              gagaCGCACGCCACAAGCACCTTCCATATAGAGGATCGGGGCCACGCGCGCTTTCACGCCTTCGAGACg  <  1:2569634/69‑1 (MQ=255)
                                                              gagaCGCACGCCACAAGCACCTTCCATATAGAGGATCGGGGCCACGCGCGCTTTCACGCCTTCGAGACg  <  1:751294/69‑1 (MQ=255)
                                                              gagaCGCACGCCACAAGCACCTTCCATATAGAGGATCGGGGCCACGCGCGCTTTCACGCCTTCGAGACg  >  1:1333376/1‑69 (MQ=255)
                                                              gagaCGCACGCCACAAGCACCTTCCATATAGAGGATCGGGGCCACGCGCGCTTTCACGCCTTCGAGACg  <  1:1915124/69‑1 (MQ=255)
                                                              gagaCGCACGCCACAAGCACCTTCCATATAGAGGATCGGGGCCACGCGCGCTTTCACGCCTTCGAGACg  >  1:812347/1‑69 (MQ=255)
                                                              gagaCGCACGCCACAAGCACCTTCCATATAGAGGATCGGGGCCACGCGCGCTTTCACGCCTTCGAGACg  >  1:882932/1‑69 (MQ=255)
                                                              gagaCGCACGCCACAAGCACCTTCCATATAGAGGATCGGGGCCACGCGCGCTTTCACGCCTTCGAGACg  <  1:2401981/69‑1 (MQ=255)
                                                              gagaCGCACGCCACAAGCACCTTCCATATAGAGGATCGGGGCCACGCGCGCTTTCACGCCTTCGAGACg  <  1:1171511/69‑1 (MQ=255)
                                                              |                                                                    
TAACCCAGCGAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCACCTTCCATATAGAGGATCGGGGCCACGCGCGCTTTCACGCCTTCGAGACG  >  minE/2902573‑2902703

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