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 2,884,233 G→A 30.7% Y125Y (TAC→TAT)  cpdB ← 2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,884,2330GA30.7% 156.0 / 77.4 159Y125Y (TAC→TAT) cpdB2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase
Reads supporting (aligned to +/- strand):  ref base G (31/79);  new base A (36/13);  total (67/92)
Fisher's exact test for biased strand distribution p-value = 1.14e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.17e-01

Only 100 of 161 total aligned reads displayed.

AATGACGTTGGCATTTACATAAGGGAATTTCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTATTTAA  >  minE/2884179‑2884298
                                                      |                                                                 
aaTGACGTTGGCATTTACATAAGGGAATTTCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTa                                                     >  1:691740/1‑69 (MQ=255)
    aCGTTGGCATTTACATAAGGGAATTTCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTa                                                 <  1:780964/69‑1 (MQ=255)
    aCGTTGGCATTTACATAAGGGAATTTCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTa                                                 <  1:1449549/69‑1 (MQ=255)
    aCGTTGGCATTTACATAAGGGAATTTCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTa                                                 <  1:579496/69‑1 (MQ=255)
    aCGTTGGCATTTACATAAGGGAATTTCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTa                                                 <  1:2699372/69‑1 (MQ=255)
       ttGGCATTTACATAAGGGAATTTCGCTCCCGCCAGCGCATTTTTCAGATAATCCAGACCGTAGTTAAAc                                              <  1:3100550/69‑1 (MQ=255)
       ttGGCATTTACATAAGGGAATTTCGCTCCCGCCAGCGCATTTTTCAGATAATCCAGACCGTAGTTAAAc                                              <  1:3403236/69‑1 (MQ=255)
       ttGGCATTTACATAAGGGAATTTCGCTCCCGCCAGCGCATTTTTCAGATAATCCAGACCGTAGTTAAAc                                              <  1:1581303/69‑1 (MQ=255)
       ttGGCATTTACATAAGGGAATTTCGCTCCCGCCAGCGCATTTTTCAGATAATCCAGACCGTAGTTAAAc                                              <  1:45748/69‑1 (MQ=255)
       ttGGCATTTACATAAGGGAATTTCGCTCCCGCCAGCGCATTTTTCAGATAATCCAGACCGTAGTTAAAc                                              <  1:889106/69‑1 (MQ=255)
       ttGGCATTTACATAAGGGAATTTCGCTCCCGCCAGCGCATTTTTCAGATAATCCAGACCGTAGTTAAAc                                              <  1:1741061/69‑1 (MQ=255)
       ttGGCATTTACATAAGGGAATTTCGCTCCCGCCAGCGCATTTTTCAGATAATCCAGACCGTAGTTAAAc                                              <  1:2030050/69‑1 (MQ=255)
       ttGGCATTTACATAAGGGAATTTCGCTCCCGCCAGCGCATTTTTCAGATAATCCAGACCGTAGTTAAAc                                              <  1:2453136/69‑1 (MQ=255)
       ttGGCATTTACATAAGGGAATTTCGCTCCCGCCAGCGCATTTTTCAGATAATCCAGACCGTAGTTAAAc                                              <  1:2181456/69‑1 (MQ=255)
        tGGCATTTACATAAGGGAATTTCGCTCCCGCCAGCGCATTTTTCAGATAATCCAGACCGTAGTTAAAc                                              <  1:1327225/68‑1 (MQ=255)
            aTTTACATAAGGGAATTTCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTg                                         <  1:320888/69‑1 (MQ=255)
               tACATAAGGGAATTTCGCTCCTGCCAGCGCATTTTTCAGGt                                                                  >  1:807538/1‑41 (MQ=255)
               tACATAAGGGAATTTCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGtt                                      >  1:2634381/1‑69 (MQ=255)
               tACATAAGGGAATTTCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGtt                                      >  1:2560452/1‑69 (MQ=255)
               tACATAAGGGAATTTCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGtt                                      >  1:2923648/1‑69 (MQ=255)
               tACATAAGGGAATTTCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGtt                                      >  1:2157527/1‑69 (MQ=255)
               tACATAAGGGAATTTCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGtt                                      >  1:2427251/1‑69 (MQ=255)
               tACATAAGGGAATTTCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGtt                                      >  1:1388624/1‑69 (MQ=255)
               tACATAAGGGAATTTCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGtt                                      >  1:130886/1‑69 (MQ=255)
                     aGGGAATTTCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTa                                                 <  1:520419/52‑1 (MQ=255)
                     aGGGAATTTCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTg                                         >  1:2086780/1‑60 (MQ=255)
                       ggAATTTCGCTCCTGCCAGCTCATTTTTCAGGTAATCCAGACCGTAGTTa                                                 <  1:790752/50‑1 (MQ=255)
                        gAATTTCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGt                             <  1:2786271/69‑1 (MQ=255)
                        gAATTTCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGt                             <  1:813984/69‑1 (MQ=255)
                        gAATTTCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGt                             <  1:1937481/69‑1 (MQ=255)
                        gAATTTCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGt                             <  1:1021171/69‑1 (MQ=255)
                        gAATTTCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGt                             >  1:930097/1‑69 (MQ=255)
                          aTTTCGCTCCCGCCAGCGCATTTTTCAGATAATCCAGACCGTAGTTAAACtt                                            >  1:2077093/1‑51 (MQ=39)
                          aTTTCGCTCCCGCCAGCGCATTTTTCAGATAATCCAGACCGTAGTTAAACt                                             >  1:186667/1‑51 (MQ=39)
                          aTTTCGCTCCCGCCAGCGCATTTTTCAGATAATCCAGACCGTAGTTAAACTc                                            >  1:2492044/1‑52 (MQ=39)
                          aTTTCGCTCCCGCCAGCGCATTTTTCAGATAATCCAGACCGTAGTTAAACTc                                            >  1:850205/1‑52 (MQ=39)
                          aTTTCGCTCCCGCCAGCGCATTTTTCAGATAATCCAGACCGTAGTTAAACTc                                            >  1:671686/1‑52 (MQ=39)
                          aTTTCGCTCCCGCCAGCGCATTTTTCAGATAATCCAGACCGTAGTTAAACTc                                            >  1:2865100/1‑52 (MQ=39)
                          aTTTCGCTCCCGCCAGCGCATTTTTCAGATAATCCAGACCGTAGTTAAACTc                                            >  1:548395/1‑52 (MQ=39)
                          aTTTCGCTCCCGCCAGCGCATTTTTCAGATAATCCAGACCGTAGTTAAACTc                                            >  1:1260814/1‑52 (MQ=39)
                          aTTTCGCTCCCGCCAGCGCATTTTTCAGATAATCCAGACCGTAGTTAAACTc                                            >  1:1945293/1‑52 (MQ=39)
                            ttCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCg                         >  1:3374398/1‑69 (MQ=255)
                            ttCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCg                         >  1:3261968/1‑69 (MQ=255)
                                 tCCTGCGAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACgg                     <  1:3070933/68‑1 (MQ=255)
                                 tCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACgg                     <  1:2225422/68‑1 (MQ=255)
                                 tCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACgg                     <  1:1046551/68‑1 (MQ=255)
                                 tCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACgg                     <  1:1619617/68‑1 (MQ=255)
                                 tCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACgg                     <  1:1894224/68‑1 (MQ=255)
                                 tCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACgg                     <  1:1820988/68‑1 (MQ=255)
                                  ccTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGta                   <  1:308268/69‑1 (MQ=255)
                                  ccTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGta                   <  1:438519/69‑1 (MQ=255)
                                  ccTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGta                   <  1:3132839/69‑1 (MQ=255)
                                  ccTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGta                   <  1:2906317/69‑1 (MQ=255)
                                  ccTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGta                   <  1:1836710/69‑1 (MQ=255)
                                  ccTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGta                   <  1:2205241/69‑1 (MQ=255)
                                  ccTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGta                   <  1:2345146/69‑1 (MQ=255)
                                  ccTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGta                   <  1:2623682/69‑1 (MQ=255)
                                   cTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGta                   <  1:673243/68‑1 (MQ=255)
                                        aGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTc              <  1:1088022/68‑1 (MQ=255)
                                        aGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTc              <  1:1423080/68‑1 (MQ=255)
                                            cATTTTTCAGATAATCCAGACCGTAGTTAAACTCGTg                                         >  1:383091/1‑37 (MQ=255)
                                            cATTTTTCAGATAATCCAGACCGTAGTTAAACTCGTg                                         >  1:3199874/1‑37 (MQ=255)
                                            cATTTTTCAGATAATCCAGACCGTAGTTAAACTCGTg                                         >  1:2429329/1‑37 (MQ=255)
                                            cATTTTTCAGATAATCCAGACCGTAGTTAAACTCGTg                                         >  1:2385798/1‑37 (MQ=255)
                                            cATTTTTCAGATAATCCAGACCGTAGTTAAACTCGTg                                         >  1:3422874/1‑37 (MQ=255)
                                            cATTTTTCAGATAATCCAGACCGTAGTTAAACTCGTg                                         >  1:376176/1‑37 (MQ=255)
                                            cATTTTTCAGATAATCCAGACCGTAGTTAAACTCGTg                                         >  1:967300/1‑37 (MQ=255)
                                            cATTTTTCAGATAATCCAGACCGTAGTTAAACTCGTg                                         >  1:2376299/1‑37 (MQ=255)
                                            cATTTTTCAGATAATCCAGACCGTAGTTAAACTCGTg                                         >  1:468874/1‑37 (MQ=255)
                                            cATTTTTCAGATAATCCAGACCGTAGTTAAACTCGTg                                         >  1:508727/1‑37 (MQ=255)
                                            cATTTTTCAGATAATCCAGACCGTAGTTAAACTCGTg                                         >  1:1480102/1‑37 (MQ=255)
                                            cATTTTTCAGATAATCCAGACCGTAGTTAAACTCGTg                                         >  1:300464/1‑37 (MQ=255)
                                            cATTTTTCAGATAATCCAGACCGTAGTTAAACTCGTg                                         >  1:705014/1‑37 (MQ=255)
                                            cATTTTTCAGATAATCCAGACCGTAGTTAAACTCGTg                                         >  1:178701/1‑37 (MQ=255)
                                            cATTTTTCAGATAATCCAGACCGTAGTTAAACTCGTg                                         >  1:2573814/1‑37 (MQ=255)
                                                tttCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGt        <  1:2099669/66‑1 (MQ=255)
                                                tttCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGt        <  1:63567/66‑1 (MQ=255)
                                                tttCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGt        <  1:1404704/66‑1 (MQ=255)
                                                tttCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGt        <  1:3074983/66‑1 (MQ=255)
                                                  tCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTAttt    <  1:1343914/68‑1 (MQ=255)
                                                  tCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTAttt    <  1:748034/68‑1 (MQ=255)
                                                  tCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTAttt    <  1:1121677/68‑1 (MQ=255)
                                                  tCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTAttt    <  1:2324358/68‑1 (MQ=255)
                                                  tCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTAttt    <  1:1610136/68‑1 (MQ=255)
                                                  tCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTAttt    <  1:1574674/68‑1 (MQ=255)
                                                  tCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTAttt    <  1:1580471/68‑1 (MQ=255)
                                                  tCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTAttt    <  1:1662550/68‑1 (MQ=255)
                                                  tCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTAttt    <  1:2207097/68‑1 (MQ=255)
                                                  tCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTAttt    <  1:3031889/68‑1 (MQ=255)
                                                  tCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTAttt    <  1:1718485/68‑1 (MQ=255)
                                                  tCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTAttt    <  1:2499703/68‑1 (MQ=255)
                                                  tCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTAttt    <  1:281164/68‑1 (MQ=255)
                                                  tCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTAttt    <  1:2765449/68‑1 (MQ=255)
                                                  tCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTAttt    <  1:2617379/68‑1 (MQ=255)
                                                  tCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTAttt    <  1:2679108/68‑1 (MQ=255)
                                                  tCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTAttt    <  1:1887423/68‑1 (MQ=255)
                                                    aGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTATTTaa  <  1:2504781/68‑1 (MQ=255)
                                                    aGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTATTTaa  <  1:1486421/68‑1 (MQ=255)
                                                    aGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTATTTaa  <  1:1280637/68‑1 (MQ=255)
                                                    aGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTATTTaa  <  1:1033516/68‑1 (MQ=255)
                                                      |                                                                 
AATGACGTTGGCATTTACATAAGGGAATTTCGCTCCTGCCAGCGCATTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTATAGTCCAGCGTATTTAA  >  minE/2884179‑2884298

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