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
A5 F1 I1 R1 81 47.9 2225048 94.8% 2109345 113.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,428,875 T→C pseudogene (80/189 nt) lomR → pseudogene, Rac prophage lom homolog,Phage or Prophage Related, interrupted by IS5 and N‑ter deletion

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,428,8750TC97.4% 141.3 / ‑4.2 39pseudogene (80/189 nt)lomRpseudogene, Rac prophage lom homolog,Phage or Prophage Related, interrupted by IS5 and N‑ter deletion
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (20/18);  total (21/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.74e-01

ATGCGCTCCGGATGAATATGATGATCTCATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGTGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGAC  >  NC_000913/1428741‑1429010
                                                                                                                                      |                                                                                                                                       
aTGCGCTCCGGATGAATATGATGATCTCATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAg                                                                                                                                     >  2:158477/1‑139 (MQ=255)
   cgcTCCGGATGAATATGATGATCTCATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGttt                                                                                                                                  >  1:1071469/1‑139 (MQ=255)
                   gatgatCTCATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCg                                                                                                                  <  1:98347/139‑1 (MQ=255)
                    atgatCTCATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGCCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGt                                                                                                                 >  2:585560/1‑139 (MQ=255)
                       atCTCATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGc                                                                                                              <  1:45057/139‑1 (MQ=255)
                        tctcATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCg                                                                                                                  <  2:493612/134‑1 (MQ=255)
                        tctcATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCg                                                                                                                  >  1:493612/1‑134 (MQ=255)
                        tctcATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGcc                                                                                                             >  2:207233/1‑139 (MQ=255)
                        tctcATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGCCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGcc                                                                                                             <  1:585560/139‑1 (MQ=255)
                          tcATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACACACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCAt                                                                                                           >  2:334942/1‑139 (MQ=255)
                           cATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCAtt                                                                                                          >  1:372749/1‑139 (MQ=255)
                               tCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGata                                                                                                      <  2:1057893/139‑1 (MQ=255)
                               tCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGata                                                                                                      <  1:992349/139‑1 (MQ=255)
                                      cTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTa                                                                                               >  1:1008488/1‑139 (MQ=255)
                                          ttCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGTGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGaa                                                                                           >  1:112106/1‑139 (MQ=255)
                                          ttCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGaa                                                                                           <  2:1008488/139‑1 (MQ=255)
                                           tCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAg                                                                                          >  1:327759/1‑139 (MQ=255)
                                               aCCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGccc                                                                                      >  2:1071093/1‑139 (MQ=255)
                                                             aaaaCGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGcc                                                                                                             >  2:75968/1‑102 (MQ=255)
                                                             aaaaCGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGcc                                                                                                             <  1:75968/102‑1 (MQ=255)
                                                             aaaaCGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATGGCTTATGAAGGCCCCGGCAGTGGCGACt                                                                        >  2:561415/1‑139 (MQ=255)
                                                                     cgacgTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACt                                                                <  1:334942/139‑1 (MQ=255)
                                                                                      gTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTggg                                               <  2:1071469/139‑1 (MQ=255)
                                                                                           gaCGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCg                                          <  2:515595/139‑1 (MQ=255)
                                                                                                tCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTtat                                     >  1:676988/1‑139 (MQ=255)
                                                                                                 cGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTtata                                    >  1:828873/1‑139 (MQ=255)
                                                                                                   ccACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCg                                                                                                                  <  1:88910/59‑1 (MQ=255)
                                                                                                   ccACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCg                                                                                                                  >  2:88910/1‑59 (MQ=255)
                                                                                                   ccACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAg                                  <  2:676988/139‑1 (MQ=255)
                                                                                                    cacaGCAACACGTCTCTGGCGTGGGGAGCTGGCACGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGt                                 <  1:457816/139‑1 (MQ=255)
                                                                                                         cAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGa                            <  2:327759/139‑1 (MQ=255)
                                                                                                                         tGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAAcaca            >  2:489973/1‑139 (MQ=255)
                                                                                                                           gggAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATg                                                                                             <  2:978087/56‑1 (MQ=255)
                                                                                                                           gggAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATg                                                                                             >  1:978087/1‑56 (MQ=255)
                                                                                                                           gggAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAgg                   >  1:1097169/1‑130 (MQ=255)
                                                                                                                           gggAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAgg                   <  2:1097169/130‑1 (MQ=255)
                                                                                                                           gggAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAgt          >  2:861269/1‑139 (MQ=255)
                                                                                                                                cTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTAt     >  2:112626/1‑139 (MQ=255)
                                                                                                                                 tGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGaa                                                                                           <  1:822427/52‑1 (MQ=255)
                                                                                                                                 tGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGaa                                                                                           >  2:822427/1‑52 (MQ=255)
                                                                                                                                   gcgcgcAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGAc  >  1:838095/1‑139 (MQ=255)
                                                                                                                                      |                                                                                                                                       
ATGCGCTCCGGATGAATATGATGATCTCATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGTGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGAC  >  NC_000913/1428741‑1429010

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A