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
A11 F1 I2 R1 59 52.6 2411032 94.1% 2268781 113.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,763,869 (T)7→8 coding (1285/1617 nt) yfjL ← CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,763,8621.T98.3% 199.0 / ‑3.6 58coding (1292/1617 nt)yfjLCP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base T (27/30);  total (28/30)
Fisher's exact test for biased strand distribution p-value = 4.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.38e-01

TAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATCACCTTCTGG  >  NC_000913/2763737‑2763995
                                                                                                                              |                                                                                                                                      
tAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTgcgcg                                                                                                                           <  1:644492/139‑1 (MQ=255)
 agagTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTgcgcgc                                                                                                                          <  2:822082/139‑1 (MQ=255)
 agagTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTgcgcgc                                                                                                                          >  2:237551/1‑139 (MQ=255)
 agagTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTgcgcgc                                                                                                                          <  1:591725/139‑1 (MQ=255)
 agagTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTgcgcgc                                                                                                                          >  2:253169/1‑139 (MQ=255)
   agTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCgg                                                                                                                        >  1:907199/1‑139 (MQ=255)
   agTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCgg                                                                                                                        <  1:253169/139‑1 (MQ=255)
     tCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTa                                                                                                                      >  1:409464/1‑139 (MQ=255)
                       acaAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATg                                                                                                    <  1:237551/139‑1 (MQ=255)
                          aaCGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTgcgcg                                                                                                                           <  1:1129241/113‑1 (MQ=255)
                          aaCGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTgcgcg                                                                                                                           >  2:1129241/1‑113 (MQ=255)
                          aaCGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTcc                                                                                                 <  2:907199/139‑1 (MQ=255)
                                aaaCGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTAc                                                                                           >  1:296539/1‑139 (MQ=255)
                                     aTCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTg                                                                                      >  2:683724/1‑139 (MQ=255)
                                       cGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGAt                                                                                    >  2:101527/1‑139 (MQ=255)
                                              aGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTAt                                                                             >  1:952968/1‑139 (MQ=255)
                                                cATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTAtctc                                                                          >  1:972426/1‑139 (MQ=255)
                                                     aaaGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACt                                                                                       <  2:895648/122‑1 (MQ=255)
                                                     aaaGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACt                                                                                       >  1:895648/1‑122 (MQ=255)
                                                     aaaGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGc                                                                      >  2:649061/1‑139 (MQ=255)
                                                      aaGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCa                                                                     >  1:1134106/1‑139 (MQ=255)
                                                          ttGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCt                                                                 >  1:66635/1‑139 (MQ=255)
                                                             gCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATc                                                                  >  1:429524/1‑135 (MQ=255)
                                                             gCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATc                                                                  <  2:429524/135‑1 (MQ=255)
                                                               tGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACgg                                                            <  2:66635/139‑1 (MQ=255)
                                                                gCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGc                                                           <  2:409464/139‑1 (MQ=255)
                                                                gCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGc                                                           <  1:149359/139‑1 (MQ=255)
                                                                 ccATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCa                                                          <  2:301919/139‑1 (MQ=255)
                                                                 ccATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCa                                                          <  2:1134106/139‑1 (MQ=255)
                                                                 ccATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCa                                                          <  2:822979/139‑1 (MQ=255)
                                                                 ccATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCa                                                          <  1:101527/139‑1 (MQ=255)
                                                                         aaTTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAat                                                  <  1:1170174/139‑1 (MQ=255)
                                                                              cGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTcc                                                                                                 >  2:1007707/1‑87 (MQ=255)
                                                                              cGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTcc                                                                                                 <  1:1007707/87‑1 (MQ=255)
                                                                              cGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAAt                                                        >  2:472276/1‑128 (MQ=255)
                                                                              cGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAAt                                                        <  1:472276/128‑1 (MQ=255)
                                                                                         tGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGc                                                           <  2:480146/115‑1 (MQ=255)
                                                                                         tGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGc                                                           >  1:480146/1‑115 (MQ=255)
                                                                                         tGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTgcgcg                                                                                                                           <  2:748465/50‑1 (MQ=255)
                                                                                         tGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTgcgcg                                                                                                                           >  1:748465/1‑50 (MQ=255)
                                                                                         tGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCg                                  >  2:603893/1‑139 (MQ=255)
                                                                                           gCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCt                                <  1:649061/139‑1 (MQ=255)
                                                                                              aaGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTAc                                                                                           >  2:354588/1‑77 (MQ=255)
                                                                                              aaGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTAc                                                                                           <  1:354588/77‑1 (MQ=255)
                                                                                                gCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGc                           <  2:952968/139‑1 (MQ=255)
                                                                                                gCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGc                           <  2:296539/139‑1 (MQ=255)
                                                                                                             gTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATc                      <  2:987965/131‑1 (MQ=255)
                                                                                                             gTCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATc                      >  1:987965/1‑131 (MQ=255)
                                                                                                              tCTTTAATGTCGAGGTT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTcc                                                                                                 <  2:799385/55‑1 (MQ=255)
                                                                                                              tCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTcc                                                                                                 >  1:799385/1‑55 (MQ=255)
                                                                                                              tCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTATAACTGATCCCGTATCTCCGGCAATCTGACGGCa                                                          >  2:413974/1‑94 (MQ=255)
                                                                                                              tCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTATAACTGATCCCGTATCTCCGGCAATCTGACGGCa                                                          <  1:413974/94‑1 (MQ=255)
                                                                                                              tCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACaa                                                                                         <  1:919203/63‑1 (MQ=255)
                                                                                                              tCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACaa                                                                                         >  2:919203/1‑63 (MQ=255)
                                                                                                              tCTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGa             >  1:70091/1‑139 (MQ=255)
                                                                                                               cTTTAATGTCGAGGAT‑TTTTTTTGTGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGAt            >  1:417654/1‑139 (MQ=255)
                                                                                                               cTTTAATGTCGAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGAt            <  2:282844/139‑1 (MQ=255)
                                                                                                                         gAGGAT‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATCACCTTCTgg  >  1:436658/1‑139 (MQ=255)
                                                                                                                              |                                                                                                                                      
TAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATCACCTTCTGG  >  NC_000913/2763737‑2763995

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A