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
A8 F50 I1 R1 163 55.0 1534755 98.6% 1513268 150.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,563,357 A→G intergenic (+240/‑235) yffP → / → yffQ CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,563,3570AG97.8% 163.3 / ‑4.3 46intergenic (+240/‑235)yffP/yffQCPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base G (17/28);  total (17/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

GCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCACAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAA  >  NC_000913/2563210‑2563502
                                                                                                                                                   |                                                                                                                                                 
gCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGcgca                                                                                                                                                 <  2:475529/150‑1 (MQ=255)
gCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGcgca                                                                                                                                                 <  1:604630/150‑1 (MQ=255)
  aaaTTTTCCAGATTTCTCGTACACGCGCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCGGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTTATGGCCGCCGACGTTGCGCAAtt                                                                                                                                              <  2:597969/151‑1 (MQ=255)
        tCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTa                                                                                                                                         <  1:59521/150‑1 (MQ=255)
            gATTTCACGTACACGCGCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAAttt                                                                                                                                     >  1:720111/1‑150 (MQ=255)
             aTTTCACGTACACGCGCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCt                                                                                                                                   <  1:291808/151‑1 (MQ=255)
             aTTTCACGTACACGCGCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCt                                                                                                                                   >  2:544198/1‑151 (MQ=255)
                        acGCGCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCaaa                                                                                                                        <  1:667036/151‑1 (MQ=255)
                         cgcgCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAAt                                                                                                                       <  1:132995/151‑1 (MQ=255)
                            gcCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCaa                                                                                                                    <  2:616419/151‑1 (MQ=255)
                               aaaaaTAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTc                                                                                                                 >  1:346134/1‑151 (MQ=255)
                                  aaTAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTcc                                                                                                                >  2:682265/1‑149 (MQ=255)
                                     aaaGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCccacca                                                                                                           <  1:651517/151‑1 (MQ=255)
                                       aGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCaaa                                                                                                         <  1:549733/151‑1 (MQ=255)
                                        ggCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCaa                                                                                                          >  1:140325/1‑149 (MQ=255)
                                           ccAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGcc                                                                                                      >  1:247095/1‑150 (MQ=255)
                                               gCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCcaaca                                                                                                  >  2:539584/1‑150 (MQ=255)
                                                  gTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGAt                                                                                              <  2:606723/151‑1 (MQ=255)
                                                  gTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGAt                                                                                              <  1:288197/151‑1 (MQ=255)
                                                    tAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATgg                                                                                            >  1:225510/1‑151 (MQ=255)
                                                    tAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATgg                                                                                            >  1:506524/1‑151 (MQ=255)
                                                     aGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATggg                                                                                           <  2:611153/151‑1 (MQ=255)
                                                        aaCCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAgg                                                                                        >  1:611089/1‑151 (MQ=255)
                                                               ccGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAAttt                                                                                 <  2:393875/151‑1 (MQ=255)
                                                               ccGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAAttt                                                                                 <  1:453782/151‑1 (MQ=255)
                                                                   gCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTtgtg                                                                             <  2:402400/151‑1 (MQ=255)
                                                                           cacaATCCCCGCTGACAGTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGa                                                                      <  1:58452/150‑1 (MQ=255)
                                                                             caATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATc                                                                    <  2:153869/150‑1 (MQ=255)
                                                                              aaTCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGc                                                                  <  2:290000/151‑1 (MQ=255)
                                                                                tCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCtt                                                                >  2:108208/1‑151 (MQ=255)
                                                                                           aTTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCa                                                      <  2:503038/150‑1 (MQ=255)
                                                                                              atatCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCa                                                  <  1:756902/151‑1 (MQ=255)
                                                                                               tatCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCAt                                                 >  1:632355/1‑151 (MQ=255)
                                                                                                   aCCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCAttttt                                             >  2:539208/1‑151 (MQ=255)
                                                                                                    cccATCTTTCCGGTTTCAGGTGGGGGACTGATTGCCGCCGGCGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGAAGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCAttt                                               <  1:9766/148‑1 (MQ=255)
                                                                                                     ccATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGt                                           <  1:656558/151‑1 (MQ=255)
                                                                                                           ttCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTaa                                       <  1:388175/149‑1 (MQ=255)
                                                                                                                 tttCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATtcaatc                                <  2:218805/150‑1 (MQ=255)
                                                                                                                 tttCAGGTGGGAGACTGATGGCCGACGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATtcaatc                                >  2:580396/1‑150 (MQ=255)
                                                                                                                    cAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACg                            >  2:105586/1‑151 (MQ=255)
                                                                                                                     aGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGa                           <  1:709990/151‑1 (MQ=255)
                                                                                                                           gagaCTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCa                     <  1:661783/151‑1 (MQ=255)
                                                                                                                             gaCTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGt                   >  2:702627/1‑151 (MQ=255)
                                                                                                                                     gccgccGACGTTGCACAATCTATTAATATCTAATCATTCAAATCAACTCCCACCAAAGCCAACAAGATGGTAGGTGAAGTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCcaa             <  2:388447/149‑1 (MQ=255)
                                                                                                                                        gccgACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCcaacaac         >  2:166406/1‑150 (MQ=255)
                                                                                                                                         ccgACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCcaacaacaa       <  1:314819/151‑1 (MQ=255)
                                                                                                                                             cGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATa   <  1:605411/151‑1 (MQ=255)
                                                                                                                                              gTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATaa  <  1:67073/151‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                                                 
GCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCACAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAA  >  NC_000913/2563210‑2563502

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A