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
A13 F1 I1 R1 778 68.7 3228504 93.4% 3015422 109.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,139,406 Δ1 bp coding (1029/1644 nt) flgK → flagellar hook‑filament junction protein 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,139,4060T.100.0% 232.5 / NA 57coding (1029/1644 nt)flgKflagellar hook‑filament junction protein 1
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (26/31);  total (26/31)

GACAACTGGCGCTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGGTGACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAATACCACTTTTACGGTGACGCCGGAT  >  NC_000913/1139273‑1139538
                                                                                                                                      |                                                                                                                                    
gACAACTGGCGCTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGtt                                                                                                                                >  2:1105355/1‑139 (MQ=255)
     cTGGCGCTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGAt                                                                                                                           <  2:95515/139‑1 (MQ=255)
     cTGGCGCTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGAt                                                                                                                           <  2:1409829/139‑1 (MQ=255)
         cgcTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGt                                                                                                                       >  1:1251708/1‑139 (MQ=255)
          gcTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGTGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTg                                                                                                                      >  2:1450038/1‑139 (MQ=255)
           cTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGc                                                                                                                     <  1:348900/139‑1 (MQ=255)
                       gAGGGTTGCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCC‑GGTGAAGATTTCTTTGCTAGCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGa                                                                                                         <  2:1215731/139‑1 (MQ=255)
                          gCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGc                                                                                                      >  2:1466205/1‑139 (MQ=255)
                            tttCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCt                                                                                                    <  1:275190/139‑1 (MQ=255)
                                     ccAACACAAAGCCGGATTTGATGCTAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTAc                                                                                           >  1:1177440/1‑139 (MQ=255)
                                       aaCACAAAGCCGGATTTGATGCTAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTg                                                                                         >  1:863721/1‑139 (MQ=255)
                                        acacAAAGCCGGATTTGATGCTAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTgg                                                                                        >  2:867094/1‑139 (MQ=255)
                                           caAAGCCGGATTTGATGCTAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGa                                                                                     <  1:1105355/139‑1 (MQ=255)
                                           caAAGCCGGATTTGATGCTAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGa                                                                                     <  1:1052372/139‑1 (MQ=255)
                                             aaGCCGGATTTGATGCTAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACa                                                                                   <  1:539189/139‑1 (MQ=255)
                                             aaGCCGGATTTGATGCTAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACa                                                                                   <  1:250161/139‑1 (MQ=255)
                                               gCCGGATTTGATGCTAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGa                                                                                 <  2:1292694/139‑1 (MQ=255)
                                                        gATGCTAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAAt                                                                        >  1:130392/1‑139 (MQ=255)
                                                          tGCTAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAAtct                                                                      <  2:819930/139‑1 (MQ=255)
                                                           gCTAACGGCGATGCCGGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAAtct                                                                      >  2:1149254/1‑139 (MQ=255)
                                                            cTAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCg                                                                    <  1:54561/139‑1 (MQ=255)
                                                             tAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGa                                                                                     <  2:524054/121‑1 (MQ=255)
                                                             tAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGa                                                                                     >  1:524054/1‑121 (MQ=255)
                                                               aCGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTc                                                                 >  2:814300/1‑139 (MQ=255)
                                                                cGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCg                                                                <  2:271965/139‑1 (MQ=255)
                                                                    gATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGataa                                                            <  1:1599447/139‑1 (MQ=255)
                                                                      tGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGc                                                                                                                     >  1:707206/1‑80 (MQ=255)
                                                                      tGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGc                                                                                                                     <  2:707206/80‑1 (MQ=255)
                                                                      tGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGa                                                                                 <  2:357949/116‑1 (MQ=255)
                                                                      tGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGa                                                                                 >  1:357949/1‑116 (MQ=255)
                                                                        cc‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATaataat                                                        <  2:1156498/139‑1 (MQ=255)
                                                                                 gATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCa                                                <  1:867094/139‑1 (MQ=255)
                                                                                 gATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCa                                                <  1:1466205/139‑1 (MQ=255)
                                                                                     tCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTc                                            <  2:1177440/139‑1 (MQ=255)
                                                                                     tCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTc                                            >  2:14631/1‑139 (MQ=255)
                                                                                            tATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGa                                                                                 >  1:114657/1‑95 (MQ=255)
                                                                                            tATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGa                                                                                 <  2:114657/95‑1 (MQ=255)
                                                                                            tATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGcc                                     <  1:565845/139‑1 (MQ=255)
                                                                                            tATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGcc                                     <  2:653274/139‑1 (MQ=255)
                                                                                                 gTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGcc                                >  2:1298951/1‑139 (MQ=255)
                                                                                                     gCCCGCGGTTCTGCAAAACACGCAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACaaaa                                                                         <  2:1358297/94‑1 (MQ=255)
                                                                                                     gCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGc                                                                                                                     >  2:1335458/1‑50 (MQ=255)
                                                                                                     gCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGc                                                                                                                     <  1:1335458/50‑1 (MQ=255)
                                                                                                     gCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACaaaa                                                                         >  1:1358297/1‑94 (MQ=255)
                                                                                                        cgcgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAATa                         >  2:912872/1‑139 (MQ=255)
                                                                                                        cgcgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAATa                         >  2:17103/1‑139 (MQ=255)
                                                                                                        cgcgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAATa                         >  1:383312/1‑139 (MQ=255)
                                                                                                        cgcgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAATa                         >  2:579368/1‑139 (MQ=255)
                                                                                                        cgcgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATAAGTGGCAGGTCACCAGCCTTGCCAGAAATa                         >  1:413535/1‑139 (MQ=255)
                                                                                                         gcgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAATAc                        <  2:130392/139‑1 (MQ=255)
                                                                                                          cgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGAt                                                                                                        <  1:13016/58‑1 (MQ=255)
                                                                                                          cgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGAt                                                                                                        >  2:13016/1‑58 (MQ=255)
                                                                                                          cgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGc                                                                                                      <  2:1040992/60‑1 (MQ=255)
                                                                                                          cgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGc                                                                                                      >  1:1040992/1‑60 (MQ=255)
                                                                                                                       cacGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGc                                 <  2:1066832/116‑1 (MQ=255)
                                                                                                                       cacGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGc                                 >  1:1066832/1‑116 (MQ=255)
                                                                                                                               aCAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAATACCACTTTTACGGTGACGCCGGAt  <  2:764904/139‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                    
GACAACTGGCGCTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCC‑GGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGGTGACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAATACCACTTTTACGGTGACGCCGGAT  >  NC_000913/1139273‑1139538

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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