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 I2 R1 764 42.0 2018750 95.5% 1927906 109.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,340,588 T→C L105S (TTA→TCA)  yrbG → putative calcium/sodium:proton antiporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,340,5880TC100.0% 176.7 / NA 49L105S (TTA→TCA) yrbGputative calcium/sodium:proton antiporter
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (25/24);  total (25/24)

ACAACGCGATTTAGCCGTTGGTACAGCCCTCGGCTCAAACATTATCAATATATTGCTGATCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATTACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGATGGTATCTTTCTCCTCTTTCTGGCTGTGCTATGGCTGCTGTTCATTGTTAAACTTGCACGTC  >  NC_000913/3340466‑3340719
                                                                                                                          |                                                                                                                                   
acaacGCGATTTAGCCGTTGGTACAGCCCTCGGCTCAAACATTATCAATATATTGCTGATCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGttgttg                                                                                                                     >  2:956238/1‑139 (MQ=255)
  aacGCGATTTAGCCGTTGGTACAGCCCTCGGCTCAAACATTATCAATATATTGCTGATCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGt                                                                                                                   <  2:875936/139‑1 (MQ=255)
                     tACAGCCCTCGGCTCAAACATTATCAATATATTGCTGATCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTcc                                                                                                <  1:406570/139‑1 (MQ=255)
                      aCAGCCCTCGGCTCAAACATTATCAATATATTGCTGATCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCg                                                                                               <  2:80355/139‑1 (MQ=255)
                               ggCTCAAACATTATCAATATATTGCTGATCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATg                                                                                      <  2:935954/139‑1 (MQ=255)
                                               atatatTGCTGATCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATg                                                                                      >  2:301443/1‑123 (MQ=255)
                                               atatatTGCTGATCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATg                                                                                      <  1:301443/123‑1 (MQ=255)
                                                tatatTGCTGATCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCAcc                                                                                                                                  >  1:351212/1‑78 (MQ=255)
                                                tatatTGCTGATCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCAcc                                                                                                                                  <  2:351212/78‑1 (MQ=255)
                                                   atTGCTGATCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGc                                                                  >  2:311818/1‑139 (MQ=255)
                                                    ttGCTGATCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGtt                                                                                                  >  1:195898/1‑106 (MQ=255)
                                                    ttGCTGATCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGtt                                                                                                  <  2:195898/106‑1 (MQ=255)
                                                     tGCTGATCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGtt                                                                                                  <  1:346224/105‑1 (MQ=255)
                                                     tGCTGATCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGtt                                                                                                  >  2:346224/1‑105 (MQ=255)
                                                     tGCTGATCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGa                                                                >  1:826771/1‑139 (MQ=255)
                                                       cTGATCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTAct                                                                                           >  1:345535/1‑110 (MQ=255)
                                                       cTGATCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTAct                                                                                           <  2:345535/110‑1 (MQ=255)
                                                       cTGATCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGATg                                                              <  2:826771/139‑1 (MQ=255)
                                                          aTCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCt                                                                                                                                >  2:526323/1‑70 (MQ=255)
                                                          aTCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCt                                                                                                                                <  1:526323/70‑1 (MQ=255)
                                                          aTCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATg                                                                                      <  2:703264/112‑1 (MQ=255)
                                                          aTCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATg                                                                                      >  1:703264/1‑112 (MQ=255)
                                                               cGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCg                                                                                                     >  2:135056/1‑92 (MQ=255)
                                                               cGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCg                                                                                                     <  1:135056/92‑1 (MQ=255)
                                                               cGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGATGGTATCtt                                                       <  1:218977/138‑1 (MQ=255)
                                                               cGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGATGGTATCtt                                                       >  2:218977/1‑138 (MQ=255)
                                                                      gCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCg                                                                                               >  1:136620/1‑91 (MQ=255)
                                                                      gCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCg                                                                                               <  2:136620/91‑1 (MQ=255)
                                                                         gcgcTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGATGGTATCTTTCTCCTCTTTc                                            <  2:429303/139‑1 (MQ=255)
                                                                         gcgcTGATTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGATGGTATCTTTCTCCTCTTTc                                            <  1:389236/139‑1 (MQ=255)
                                                                          cgcTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGATGGTATCTTTCTCCTCTTTCt                                           <  1:956238/139‑1 (MQ=255)
                                                                            cTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGATGGTATCTTTCTCCTCTTTCTgg                                         <  1:311818/139‑1 (MQ=255)
                                                                                               tCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGATgg                                                             >  1:217200/1‑100 (MQ=255)
                                                                                               tCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGATgg                                                             <  2:217200/100‑1 (MQ=255)
                                                                                               tCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGATGGTATCTTTCTCCTCTTTCTGGCTGTGCTATGGCTGCTGtt                      >  1:789017/1‑139 (MQ=255)
                                                                                               tCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGATGGTATCTTTCTCCTCTTTCTGGCTGTGCTATGGCTGCTGtt                      >  1:468886/1‑139 (MQ=255)
                                                                                               tCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGATGGTATCTTTCTCCTCTTTCTGGCTGTGCTATGGCTGCTGtt                      >  1:454796/1‑139 (MQ=255)
                                                                                               tCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGATGGTATCTTTCTCCTCTTTCTGGCTGTGCTATGGCTGCTGtt                      >  1:349363/1‑139 (MQ=255)
                                                                                               tCCATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGATGGTATCTTTCTCCTCTTTCTGGCTGTGCTATGGCTGCTGtt                      >  1:2214/1‑139 (MQ=255)
                                                                                                ccATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGATGGTa                                                           <  1:663793/101‑1 (MQ=255)
                                                                                                ccATTCTGATGTTCTACGCCGTGAATCACCCATAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGATGGTa                                                           >  2:663793/1‑101 (MQ=255)
                                                                                                 cATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATg                                                                                      >  1:524070/1‑73 (MQ=255)
                                                                                                 cATTCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATg                                                                                      <  2:524070/73‑1 (MQ=255)
                                                                                                   ttCTGATGTTCTACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGATGGTATCTTTCTCCTCTTTCTGGCTGTGCTATGGCTGCTGTTCAtt                  >  1:856847/1‑139 (MQ=255)
                                                                                                              tACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTAct                                                                                           <  1:517025/55‑1 (MQ=255)
                                                                                                              tACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTAct                                                                                           >  2:517025/1‑55 (MQ=255)
                                                                                                              tACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGAt                                                               <  1:599608/83‑1 (MQ=255)
                                                                                                              tACGCCGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGAt                                                               >  2:599608/1‑83 (MQ=255)
                                                                                                                   cGTGAATCACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGATGGTATCTTTCTCCTCTTTCTGGCTGTGCTATGGCTGCTGTTCATTGTTAAACTTGCACGTc  >  2:263391/1‑139 (MQ=255)
                                                                                                                          |                                                                                                                                   
ACAACGCGATTTAGCCGTTGGTACAGCCCTCGGCTCAAACATTATCAATATATTGCTGATCCTCGGTCTGGCTGCGCTGGTTCGTCCTTTTACCGTCCATTCTGATGTTCTACGCCGTGAATTACCCTTAATGTTGTTGGTCAGCGTGGTGGCCGGTTCCGTACTCTATGACGGACAACTTAGTCGCAGCGATGGTATCTTTCTCCTCTTTCTGGCTGTGCTATGGCTGCTGTTCATTGTTAAACTTGCACGTC  >  NC_000913/3340466‑3340719

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