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
A10 F1 I1 R1 759 65.2 3386260 90.7% 3071337 101.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 922,727 A→G intergenic (‑137/‑186) cspD ← / → clpS inhibitor of DNA replication, cold shock protein homolog/regulatory protein for ClpA substrate specificity

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913922,7270AG100.0% 188.7 / NA 53intergenic (‑137/‑186)cspD/clpSinhibitor of DNA replication, cold shock protein homolog/regulatory protein for ClpA substrate specificity
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (28/25);  total (28/25)

CTTCGACATCCTTCGCAAATCTTATACAAGTAAGATGGAATAAACCGGGGTCAGAGAGGGGGCTGTTCAAAACCTCGCCAACTCTAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGACAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCGCTGATGCCAACGATAGATGATAGTTATCTATCATGTGGAGTAGATTGGTCAGGCAAATAAGCT  >  NC_000913/922592‑922857
                                                                                                                                       |                                                                                                                                  
cTTCGACATCCTTCGCAAGTCTTATACAAGTAAGATGGAATAAACCGGGGTCAGAGAGGGGGCTGTTCAAAACCTCGCCAACTCTAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCaa                                                                                                                                 <  2:262783/139‑1 (MQ=255)
   cGACATCCTTCGCAAATCTTATACAAGTAAGATGGAATAAACCGGGGTCAGAGAGGGGGCTGTTCAAAACCTCGCCAACTCTAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAggg                                                                                                                              >  2:1662248/1‑139 (MQ=255)
          cTTCGCAAATCTTATACAAGTAAGATGGAATAAACCGGGGTCAGAGAGGGGGCTGTTCAAAACCTCGCCAACTCTAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTa                                                                                                                       >  2:820274/1‑139 (MQ=255)
                             gTAAGATGGAATAAACCGGGGTCAGAGAGGGGGCTGTTCAAAACCTCGCCAACTCTAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGc                                                                                                    >  2:447863/1‑139 (MQ=255)
                                     gAATAAACCGGGGTCAGAGAGGGGGCTGTTCAAAACCTCGCCAACTCTAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAg                                                                                                     <  1:614293/130‑1 (MQ=255)
                                     gAATAAACCGGGGTCAGAGAGGGGGCTGTTCAAAACCTCGCCAACTCTAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAg                                                                                                     >  2:614293/1‑130 (MQ=255)
                                     gAATAAACCGGGGTCAGAGAGGGGGCTGTTCAAAACCTCGCCAACTCTAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACg                                                                                            >  2:550801/1‑139 (MQ=255)
                                     gAATAAACCGGGGTCAGAGAGGGGGCTGTTCAAAACCTCGCCAACTCTAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACg                                                                                            <  1:1662248/139‑1 (MQ=255)
                                        tAAACCGGGGTCAGAGAGGGGGCTGTTCAAAACCTCGCCAACTCTAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAgggg                                                                                                                             <  2:1426817/103‑1 (MQ=255)
                                        tAAACCGGGGTCAGAGAGGGGGCTGTTCAAAACCTCGCCAACTCTAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAgggg                                                                                                                             >  1:1426817/1‑103 (MQ=255)
                                        tAAACCGGGGTCAGAGAGGGGGCTGTTCAAAACCTCGCCAACTCTAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTa                                                                                         <  1:820274/139‑1 (MQ=255)
                                               gggTCAGAGAGGGGGCTGTTCAAAACCTCGCCAACTCTAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAg                                                                                  >  2:1513780/1‑139 (MQ=255)
                                                      agagGGGGCTGTTCAAAACCTCGCCAACTCTAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAAtgtg                                                                           >  2:1246129/1‑139 (MQ=255)
                                                          ggggCTGTTCAAAACCTCGCCAACTCTAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAg                                                                       >  2:1173618/1‑139 (MQ=255)
                                                             gCTGTTCAAAACCTCGCCAACTCTAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATg                                                                    <  1:550801/139‑1 (MQ=255)
                                                                  tCAAAACCTCGCCAACTCTAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCGCt                                                               <  1:1246129/139‑1 (MQ=255)
                                                                   cAAAACCTCGCCAACTCTAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCGCTg                                                              <  1:1173618/139‑1 (MQ=255)
                                                                           cGCCAACTCTAGCAATACAATTTAGAGAATTAGGGCGAGTCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATC‑‑AAATTTGAAGCAGTTAAAGCTATTGACAGGaa                                                                               <  1:1027394/112‑1 (MQ=255)
                                                                           cGCCAACTCTAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCGCTGAt                                                            <  1:1469925/133‑1 (MQ=255)
                                                                           cGCCAACTCTAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCGCTGAt                                                            >  2:1469925/1‑133 (MQ=255)
                                                                           cGCCAACTCTAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATC‑‑AAATTTGAAGCAGTTAACGCTATTGACAGGaa                                                                               >  2:1027394/1‑112 (MQ=255)
                                                                                    tAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCGCTGATGCCAACGATAgatga                                             <  1:447863/139‑1 (MQ=255)
                                                                                         aTACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCGCTGATGCCAACGATAGATGATAGtt                                        <  1:1513780/139‑1 (MQ=255)
                                                                                           aCAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCGCTGATGCCAACGATAgatga                                             <  1:645638/132‑1 (MQ=255)
                                                                                           aCAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCGCTGATGCCAACGATAgatga                                             >  2:645638/1‑132 (MQ=255)
                                                                                            cAATTTAGAGAATTAGGGCGAGCCGTCAATCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATGTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCGCTGATGCCAACGATAGATGATAGTtatc                                     >  2:952398/1‑139 (MQ=255)
                                                                                            cAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCa                                                                                                                                  >  1:461634/1‑46 (MQ=255)
                                                                                            cAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGc                                                                                                                            <  2:266659/52‑1 (MQ=255)
                                                                                            cAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGc                                                                                                                            >  1:266659/1‑52 (MQ=255)
                                                                                            cAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGt                                                                                                 <  1:673234/79‑1 (MQ=255)
                                                                                            cAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGt                                                                                                 >  2:673234/1‑79 (MQ=255)
                                                                                            cAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCGCTGATGCCAACGATAgatga                                             >  1:827292/1‑131 (MQ=255)
                                                                                            cAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCGCTGATGCCAACGATAgatga                                             <  2:827292/131‑1 (MQ=255)
                                                                                              aTTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCg                                                                 >  2:985170/1‑109 (MQ=255)
                                                                                              aTTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCg                                                                 <  1:1191762/109‑1 (MQ=255)
                                                                                              aTTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCg                                                                 <  1:985170/109‑1 (MQ=255)
                                                                                              aTTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCg                                                                 >  2:1191762/1‑109 (MQ=255)
                                                                                                    agaATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCa                                                                                                                                  >  1:665151/1‑38 (MQ=255)
                                                                                                    agaATTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCa                                                                                                                                  <  2:665151/38‑1 (MQ=255)
                                                                                                      aaTTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCGCTGATg                                                           >  1:439179/1‑107 (MQ=255)
                                                                                                      aaTTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCGCTGATg                                                           <  2:439179/107‑1 (MQ=255)
                                                                                                       aTTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCGCTGATGCCAACGATAGATGATAGTtatcta                                   >  2:1412833/1‑130 (MQ=255)
                                                                                                       aTTAGGGCGAGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCGCTGATGCCAACGATAGATGATAGTtatcta                                   <  1:1412833/130‑1 (MQ=255)
                                                                                                                aGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGaa                                                                                                      <  2:185506/54‑1 (MQ=255)
                                                                                                                aGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGaa                                                                                                      >  1:185506/1‑54 (MQ=255)
                                                                                                                aGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCt                                                                                          >  2:1402023/1‑66 (MQ=255)
                                                                                                                aGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCt                                                                                          <  1:1402023/66‑1 (MQ=255)
                                                                                                                aGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCGCTGATGCCAACGATAGATGATAGTTATCTATCATGTGGAGTAGATTgg                 >  2:724193/1‑139 (MQ=255)
                                                                                                                aGCCGTCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCGCTGATGCCAACGATAGATGATAGTTATCTATCATGTGGAGTAGATTgg                 >  1:1340883/1‑139 (MQ=255)
                                                                                                                     tCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTAt                                                                                        <  2:658586/63‑1 (MQ=255)
                                                                                                                     tCAAGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTAt                                                                                        >  1:658586/1‑63 (MQ=255)
                                                                                                                        aGCATTTGACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCGCTGATGCCAACGATAGATGATAGTTATCTATCATGTGGAGTAGATTGGTCAGGCaa         <  2:1340883/139‑1 (MQ=255)
                                                                                                                               gACAGGGGGCAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCGCTGATGCCAACGATAGATGATAGTTATCTATCATGTGGAGTAGATTGGTCAGGCAAATAAGct  >  1:1650792/1‑139 (MQ=255)
                                                                                                                                       |                                                                                                                                  
CTTCGACATCCTTCGCAAATCTTATACAAGTAAGATGGAATAAACCGGGGTCAGAGAGGGGGCTGTTCAAAACCTCGCCAACTCTAGAAATACAATTTAGAGAATTAGGGCGAGCCGTCAAGCATTTGACAGGGGACAAGGGGCAGGTATGAATCAAAAATTTGAAGCAGTTAACGCTATTGACAGGAATGTGACAGATGTCGCTGATGCCAACGATAGATGATAGTTATCTATCATGTGGAGTAGATTGGTCAGGCAAATAAGCT  >  NC_000913/922592‑922857

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