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 1,904,641 C→T 50.0% T427T (ACG→ACA)  ptr ← protease III

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,904,6410CT50.0% 1.4 / 168.8 178T427T (ACG→ACA) ptrprotease III
Reads supporting (aligned to +/- strand):  ref base C (23/66);  new base T (33/56);  total (56/122)
Fisher's exact test for biased strand distribution p-value = 1.46e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.50e-01

Only 100 of 178 total aligned reads displayed.

TCATCATCGCCAGACGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCGTATGCTCAACAGGAACGCGAATCATGGTATCTGCCAGCCATTCGACGTAATCCATATCACGGGTG  >  minE/1904574‑1904707
                                                                   |                                                                  
tcatcaTCGCCAGACGTTCCTTTACTGGTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCg                                                                   <  1:195200/69‑1 (MQ=255)
tcatcaTCGCCAGACGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCg                                                                   <  1:2701996/69‑1 (MQ=255)
tcatcaTCGCCAGACGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCg                                                                   <  1:3362960/69‑1 (MQ=255)
tcatcaTCGCCAGACGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCg                                                                   <  1:1001537/69‑1 (MQ=255)
tcatcaTCGCCAGACGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCg                                                                   <  1:1173370/69‑1 (MQ=255)
tcatcaTCGCCAGACGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCg                                                                   <  1:531591/69‑1 (MQ=255)
tcatcaTCGCCAGACGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCg                                                                   <  1:2207518/69‑1 (MQ=255)
tcatcaTCGCCAGACGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCg                                                                   <  1:616156/69‑1 (MQ=255)
  atcatcGCCAGACGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCGt                                                                  >  1:1059595/1‑68 (MQ=255)
  atcatcGCCAGACGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCGTa                                                                 <  1:2063489/69‑1 (MQ=255)
       cGCCAGACGTTCTTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGTGTATGCTc                                                            <  1:2056110/69‑1 (MQ=255)
       cGCCAGACGTTCTTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGTGTATGCTc                                                            <  1:2111430/69‑1 (MQ=255)
       cGCCAGACGTTCTTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGTGTATGCTc                                                            <  1:1805471/69‑1 (MQ=255)
       cGCCAGACGTTCTTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGTGTATGCTc                                                            <  1:1675183/69‑1 (MQ=255)
       cGCCAGACGTTCTTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGTGTATGCTc                                                            <  1:3024567/69‑1 (MQ=255)
       cGCCAGACGTTCTTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGTGTATGCTc                                                            <  1:1044853/69‑1 (MQ=255)
       cGCCAGACGTTCTTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGTGTATGCTc                                                            <  1:2560398/69‑1 (MQ=255)
       cGCCAGACGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCGTATGCTc                                                            <  1:2938944/69‑1 (MQ=255)
       cGCCAGACGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCGTATGCTc                                                            <  1:2794330/69‑1 (MQ=255)
       cGCCAGACGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCGTATGCTc                                                            <  1:2573738/69‑1 (MQ=255)
       cGCCAGACGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCGTATGCTc                                                            <  1:1850288/69‑1 (MQ=255)
       cGCCAGACGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCGTATGCTc                                                            <  1:2840186/69‑1 (MQ=255)
       cGCCAGACGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCGTATGCTc                                                            <  1:2204279/69‑1 (MQ=255)
       cGCCAGACGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCGTATGCTc                                                            <  1:2853195/69‑1 (MQ=255)
       cGCCAGACGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCGTATGCTc                                                            <  1:1481960/69‑1 (MQ=255)
        gCCAGACGTTCTTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGTGTATGCTc                                                            <  1:659055/68‑1 (MQ=255)
             aCGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCGTATGCTCAACAgg                                                      <  1:905692/69‑1 (MQ=255)
             aCGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCGTATGCTCAACAgg                                                      >  1:3193522/1‑69 (MQ=255)
             aCGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCGTATGCTCAACAgg                                                      <  1:2440891/69‑1 (MQ=255)
              cGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCGTATGCTCAACAGGa                                                     <  1:2656396/69‑1 (MQ=255)
              cGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCGTATGCTCAACAGGa                                                     <  1:2885854/69‑1 (MQ=255)
              cGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCGTATGCTCAACAGGa                                                     <  1:1035454/69‑1 (MQ=255)
              cGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCGTATGCTCAACAGGa                                                     <  1:1189296/69‑1 (MQ=255)
                        cTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCGTATGCTCAACAGGAACGCGAAt                                             <  1:2584439/67‑1 (MQ=255)
                        cTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCGTATGCTCAACAGGAACGCGAAt                                             <  1:1081026/67‑1 (MQ=255)
                              tAGCATCGTACCGATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAAcgc                                                 >  1:428976/1‑57 (MQ=255)
                              tAGCATCGTACCGATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAAcgc                                                 >  1:1413323/1‑57 (MQ=255)
                              tAGCATCGTACCGATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAAcgc                                                 >  1:886513/1‑57 (MQ=255)
                              tAGCATCGTACCGATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAAcgc                                                 >  1:1097505/1‑57 (MQ=255)
                              tAGCATCGTACCGATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAAcgc                                                 >  1:1798107/1‑57 (MQ=255)
                              tAGCATCGTACCGATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAAcgc                                                 >  1:2175230/1‑57 (MQ=255)
                              tAGCATCGTACCGATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAAcg                                                  >  1:2296561/1‑56 (MQ=255)
                              tAGCATCGTACCGATCGGCAATATTGACTGCATCCAGTGTATGCT‑AACAGGAAcgc                                                 >  1:3360552/1‑56 (MQ=255)
                                gCATCGTACCGATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTATc                                    <  1:72381/68‑1 (MQ=255)
                                gCATCGTACCGATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTATc                                    <  1:2733763/68‑1 (MQ=255)
                                gCATCGTACCGATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTATc                                    <  1:1768732/68‑1 (MQ=255)
                                gCATCGTACCGATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTATc                                    <  1:122608/68‑1 (MQ=255)
                                gCATCGTACCGATCGGCAATATTGACTGCATCCAGCGTATGCTc                                                            <  1:3146284/44‑1 (MQ=255)
                                          gATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTATCAGCCAGCCAtt                         <  1:38896/69‑1 (MQ=255)
                                          gATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTATCAGCCAGCCAtt                         <  1:992186/69‑1 (MQ=255)
                                          gATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTATCAGCCAGCCAtt                         <  1:2833737/69‑1 (MQ=255)
                                          gATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTATCAGCCAGCCAtt                         <  1:919333/69‑1 (MQ=255)
                                          gATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTATCAGCCAGCCAtt                         <  1:821263/69‑1 (MQ=255)
                                          gATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTATCAGCCAGCCAtt                         <  1:2904718/69‑1 (MQ=255)
                                          gATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTATCAGCCAGCCAtt                         <  1:766167/69‑1 (MQ=255)
                                          gATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTATCAGCCAGCCAtt                         <  1:67071/69‑1 (MQ=255)
                                          gATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTATCAGCCAGCCAtt                         <  1:197581/69‑1 (MQ=255)
                                          gATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTATCAGCCAGCCAtt                         <  1:1068757/69‑1 (MQ=255)
                                          gATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTATCAGCCAGCCAtt                         <  1:1506484/69‑1 (MQ=255)
                                          gATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTATCAGCCAGCCAtt                         <  1:1693992/69‑1 (MQ=255)
                                          gATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTATCAGCCAGCCAtt                         <  1:1751541/69‑1 (MQ=255)
                                          gATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTATCAGCCAGCCAtt                         <  1:2145762/69‑1 (MQ=255)
                                          gATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTATCAGCCAGCCAtt                         <  1:2278288/69‑1 (MQ=255)
                                          gATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTATCAGCCAGCCAtt                         <  1:2557727/69‑1 (MQ=255)
                                          gATCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGCTATCAGCCAGCCAtt                         <  1:681060/69‑1 (MQ=255)
                                           aTCGGCAATATTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTATCAGCCAGCCAtt                         <  1:1213428/68‑1 (MQ=255)
                                                  attttGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTATCAGCCAGCCAtt                         <  1:3181935/58‑1 (MQ=255)
                                                  atatTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTa                                      >  1:2828202/1‑48 (MQ=255)
                                                  atatTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTa                                      >  1:1871882/1‑48 (MQ=255)
                                                  atatTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTa                                      >  1:1564747/1‑48 (MQ=255)
                                                  atatTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTa                                      >  1:373452/1‑48 (MQ=255)
                                                  atatTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTa                                      >  1:2684869/1‑48 (MQ=255)
                                                  atatTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTa                                      >  1:3324726/1‑48 (MQ=255)
                                                  atatTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTa                                      >  1:3297275/1‑48 (MQ=255)
                                                  atatTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTa                                      >  1:2224162/1‑48 (MQ=255)
                                                  atatTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTa                                      >  1:2427974/1‑48 (MQ=255)
                                                  atatTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTa                                      >  1:2922140/1‑48 (MQ=255)
                                                  atatTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTa                                      >  1:2452340/1‑48 (MQ=255)
                                                  atatTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTa                                      >  1:123804/1‑48 (MQ=255)
                                                  atatTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTa                                      >  1:2245406/1‑48 (MQ=255)
                                                  atatTGACTGCATCCAGTGTATGCTCAACAGGAACGCGAATCATGGTa                                      >  1:2665638/1‑48 (MQ=255)
                                                    atTGACTGCATCCAGCGTATGCTCAACAGGAACGCGAATCATGGTATCTGCCAGCCATTCGACGTAATc               >  1:549806/1‑69 (MQ=255)
                                                     ttGACTGCATCCAGCGTATGCTCAACAGGAACGCGAATCa                                           <  1:501226/40‑1 (MQ=255)
                                                     ttGACTGCATCCAGCGTATGCTCAACAGGAACGCGAATCa                                           <  1:165608/40‑1 (MQ=255)
                                                     ttGACTGCATCCAGCGTATGCTCAACAGGAACGCGAATCATGGTATCt                                   >  1:1890763/1‑48 (MQ=255)
                                                     ttGACTGCATCCAGCGTATGCTCAACAGGAACGCGAATCATGGTATCTGCCAGCCATTCGACGTaa                 <  1:2765305/66‑1 (MQ=255)
                                                     ttGACTGCATCCAGCGTATGCTCAACAGGAACGCGAATCATGGTATCTGCCAGCCATTCGACGTaa                 <  1:3080008/66‑1 (MQ=255)
                                                     ttGACTGCATCCAGCGTATGCTCAACAGGAACGCGAATCATGGTATCTGCCAGCCATTCGACGTaa                 <  1:593997/66‑1 (MQ=255)
                                                     ttGACTGCATCCAGCGTATGCTCAACAGGAACGCGAATCATGGTATCTGCCAGCCATTCGACGTaa                 <  1:2584234/66‑1 (MQ=255)
                                                     ttGACTGCATCCAGCGTATGCTCAACAGGAACGCGAATCATGGTATCTGCCAGCCATTCGACGTAATc               >  1:1648411/1‑68 (MQ=255)
                                                     ttGACTGCATCCAGCGTATGCTCAACAGGAACGCGAATCATGGTATCTGCCAGCCATTCGACGTAATc               >  1:2311865/1‑68 (MQ=255)
                                                       gACTGCATCCAGCGTATGCTCAACAGGAACGCGAATCa                                           >  1:1866067/1‑38 (MQ=255)
                                                       gACTGCATCCAGCGTATGCTCAACAGGAACGCGAATCa                                           >  1:3244988/1‑38 (MQ=255)
                                                       gACTGCATCCAGCGTATGCTCAACAGGAACGCGAATCATGGTa                                      <  1:1711566/43‑1 (MQ=255)
                                                       gACTGCATCCAGCGTATGCTCAACAGGAACGCGAATCATGGTa                                      <  1:649182/43‑1 (MQ=255)
                                                       gACTGCATCCAGCGTATGCTCAACAGGAACGCGAATCATGGTa                                      <  1:3016780/43‑1 (MQ=255)
                                                                  gCGTATGCTCAACAGGAACGCGAATCATGGTATCTGCCAGCCATTCGACGTAATCCATATCACGGGTg  <  1:425883/68‑1 (MQ=255)
                                                                  gCGTATGCTCAACAGGAACGCGAATCATGGTATCTGCCAGCCATTCGACGTAATCCATATCACGGGTg  <  1:862579/68‑1 (MQ=255)
                                                                  gCGTATGCTCAACAGGAACGCGAATCATGGTATCTGCCAGCCATTCGACGTAATCCATATCACGGGTg  <  1:3033390/68‑1 (MQ=255)
                                                                  gCGTATGCTCAACAGGAACGCGAATCATGGTATCTGCCAGCCATTCGACGTAATCCATATCACGGGTg  <  1:2277793/68‑1 (MQ=255)
                                                                   |                                                                  
TCATCATCGCCAGACGTTCCTTTACTGCTTTAGCATCGTACCGATCGGCAATATTGACTGCATCCAGCGTATGCTCAACAGGAACGCGAATCATGGTATCTGCCAGCCATTCGACGTAATCCATATCACGGGTG  >  minE/1904574‑1904707

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