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 4,061,157 G→A *237* (TAG→TAA)  yihL → putative DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,061,1570GA100.0% 197.2 / NA 61*237* (TAG→TAA) yihLputative DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (28/33);  total (28/33)

TTGGCGGTTCTGCGGGTATGCCAGCGATCTTAATTGAAAAGCATCGCGCCGACCAGCAAGGCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAGGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCTTTATTTACATGCTTATGCCTTTCATTTAAATATGCGGCTGGAAAGAGTGTTGCCTGCTGA  >  NC_000913/4061030‑4061280
                                                                                                                               |                                                                                                                           
ttGGCGGTTCTGCGGGTATGCCAGCGATCTTAATTGAAAAGCATCGCGCCGACCAGCAAGGCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATgg                                                                                                                  <  1:21712/139‑1 (MQ=255)
 tGGCGGTTCTGCGGGTATGCCAGCGACCTTAATTGAACAGCATCGCGCCGACCAGCAAGGCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGt                                                                                                                 <  1:1025554/139‑1 (MQ=255)
  ggCGGTTCTGCGGGTATGCCAGCGATCTTAATTGAAAAGCATCGCGCCGACCAGCAAGGCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTg                                                                                                                <  2:101107/139‑1 (MQ=255)
      gTTCTGCGGGTATGCCAGCGATCTTAATTGAAAAGCGTCGCGCCGACAAGCAAGGCAATATTGTCCAAATAGATATTGAATATTGGCAATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACaa                                                                                                            >  2:1025554/1‑139 (MQ=255)
            cGGGTATGCCAGCGATCTCAATTGAAAAGCATCGCGCCGACCAGCAAGGCAATATTGTCCAAATAGATATTGAGTATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACaataaata                                                                                                      >  1:975249/1‑139 (MQ=255)
                 aTGCCAGCGATCTTAATTGAAAAGCATCGCGCCGACCAGCAAGGCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATgg                                                                                                                  >  1:874372/1‑122 (MQ=255)
                 aTGCCAGCGATCTTAATTGAAAAGCATCGCGCCGACCAGCAAGGCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATgg                                                                                                                  <  2:874372/122‑1 (MQ=255)
                   gCCAGCGATCTTAATTGAAAAGCATCGCGCCGACCAGCAAGGCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCaag                                                                                               <  2:277567/139‑1 (MQ=255)
                       gCGATCTTAATTGAAAAGCATCGCGCCGACCAGCAAGGCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCaagaaag                                                                                           <  1:132730/139‑1 (MQ=255)
                                aTTGAAAAGCATCGCGCCGACCAGCAAGGCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACaa                                                                                  <  1:1586097/139‑1 (MQ=255)
                                     aaaGCATCGCGCCGACCAGCAAGGCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACgtgt                                                                             >  1:1601603/1‑139 (MQ=255)
                                     aaaGCATCGCGCCGACCAGCAAGGCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACgtgt                                                                             >  2:268181/1‑139 (MQ=255)
                                              cgcCGACCAGCAAGGCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCaagaaa                                                                                            >  2:431317/1‑115 (MQ=255)
                                              cgcCGACCAGCAAGGCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCaagaaa                                                                                            <  1:431317/115‑1 (MQ=255)
                                              cgcCGACCAGCAAGGCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCaag                                                                                               >  2:1162036/1‑112 (MQ=255)
                                              cgcCGACCAGCAAGGCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCaag                                                                                               <  1:1162036/112‑1 (MQ=255)
                                                   aCCAGCAAGGCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATg                                                                                                                   <  1:138919/87‑1 (MQ=255)
                                                   aCCAGCAAGGCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATg                                                                                                                   >  2:138919/1‑87 (MQ=255)
                                                    ccAGCAAGGCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCctct                                                              <  1:268181/139‑1 (MQ=255)
                                                        cAAGGCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCtttat                                                          <  2:1601603/139‑1 (MQ=255)
                                                           ggCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCctct                                                              >  1:582248/1‑132 (MQ=255)
                                                           ggCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCctct                                                              <  2:582248/132‑1 (MQ=255)
                                                           ggCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCtttattta                                                       <  2:975249/139‑1 (MQ=255)
                                                            gCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCTTTATTTAc                                                      <  2:1097605/139‑1 (MQ=255)
                                                             cAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCTTTATTTACa                                                     >  2:31937/1‑139 (MQ=255)
                                                                tatTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACActc                                                                     <  1:73218/120‑1 (MQ=255)
                                                                tatTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACActc                                                                     >  2:73218/1‑120 (MQ=255)
                                                                  ttGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGtt                                                                                                                        >  1:347170/1‑67 (MQ=255)
                                                                  ttGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGtt                                                                                                                        <  2:347170/67‑1 (MQ=255)
                                                                     tCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATgg                                                                                                                  <  2:1145681/70‑1 (MQ=255)
                                                                     tCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATgg                                                                                                                  >  1:1145681/1‑70 (MQ=255)
                                                                     tCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCTTTATTTACATGCTTATg                                             >  1:1072080/1‑139 (MQ=255)
                                                                     tCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCTTTATTTACATGCTTATg                                             >  1:1336048/1‑139 (MQ=255)
                                                                      ccAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCTTTATTTACATGCTTATGc                                            >  2:836598/1‑139 (MQ=255)
                                                                      ccAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCTTTATTTACATGCTTATGc                                            >  1:834455/1‑139 (MQ=255)
                                                                       cAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATgg                                                                                                                  <  1:264202/68‑1 (MQ=255)
                                                                       cAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATgg                                                                                                                  >  2:264202/1‑68 (MQ=255)
                                                                       cAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAGAGATTCTACAACGTGTCGa                                                                          <  1:260262/108‑1 (MQ=255)
                                                                       cAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAGAGATTCTACAACGTGTCGa                                                                          >  2:260262/1‑108 (MQ=255)
                                                                        aaaTAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCTTTATTTACATGCTTATGCCt                                          <  2:834455/139‑1 (MQ=255)
                                                                               tatTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCTTTATTTACATGCTTATGCCTTTCAttt                                   >  1:999649/1‑139 (MQ=255)
                                                                               tatTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCTTTATTTACATGCTTATGCCTTTCAttt                                   >  2:284784/1‑139 (MQ=255)
                                                                               tatTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCTTTATTTACATGCTTATGCCTTTCAttt                                   >  2:279475/1‑139 (MQ=255)
                                                                                        ttGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATgg                                                                                                                  >  1:849979/1‑51 (MQ=255)
                                                                                        ttGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATgg                                                                                                                  <  2:849979/51‑1 (MQ=255)
                                                                                         tGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCTTTATTTACATGCTTATGCCTTTCATTTAAATATGCgg                         >  2:1221012/1‑139 (MQ=255)
                                                                                          ggCGAGTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAACGATTCTACAACGTGTCGACACTCTTCCTCTTTATTTACATGCTTATGCCTTTCATTTAAATATGCGGc                        <  2:999649/139‑1 (MQ=255)
                                                                                           gCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCTTTATTTACATGCTTATGCCTTTCATTTAAATATGCGGCt                       <  2:1336048/139‑1 (MQ=255)
                                                                                              aTTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCTTTATTTACATGCTTATGCCTTTCATTTAAATATGCGGCTGGa                    <  1:1595337/139‑1 (MQ=255)
                                                                                              aTTTGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCTTTATTTACATGCTTATGCCTTTCATTTAAATATGCGGCTGGa                    <  2:1072080/139‑1 (MQ=255)
                                                                                               tttGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCTTTATTTACATGCTTATGCCTTTCATTTAAATATGCGGCTGGaa                   <  1:836598/139‑1 (MQ=255)
                                                                                                ttGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGt                                                                                                                 <  2:842789/44‑1 (MQ=255)
                                                                                                ttGAGGCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGt                                                                                                                 >  1:842789/1‑44 (MQ=255)
                                                                                                     gCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCtttattta                                                       <  2:36522/97‑1 (MQ=255)
                                                                                                     gCCGTAGACCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCtttattta                                                       >  1:36522/1‑97 (MQ=255)
                                                                                                            aCCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCTTTATTTACATGCTTATGCCTTTCATTTAAATATGCGGCTGGAAAGAGTGTTGCctg      <  2:1345367/139‑1 (MQ=255)
                                                                                                            aCCTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCTTTATTTACATGCTTATGCCTTTCATTTAAATATGCGGCTGGAAAGAGTGTTGCctg      <  1:1221012/139‑1 (MQ=255)
                                                                                                             ccTCATCATTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCTTTATTTACATGCTTATGCCTTTCATTTAAATATGCGGCTGGAAAGAGTGTTGCctgc     <  1:279475/139‑1 (MQ=255)
                                                                                                                catcatTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCTTTATTTACATGCTTATGCCTTTCATTTAAATATGCGGCTGGAAAGAGTGTTGCCTGCTGa  >  2:254146/1‑139 (MQ=255)
                                                                                                                 atcatTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCaagaa                                                                                             >  1:881996/1‑47 (MQ=255)
                                                                                                                 atcatTAATCTGTAAGTGTTTTATGGTGACAATAAATAACGCaagaa                                                                                             <  2:881996/47‑1 (MQ=255)
                                                                                                                               |                                                                                                                           
TTGGCGGTTCTGCGGGTATGCCAGCGATCTTAATTGAAAAGCATCGCGCCGACCAGCAAGGCAATATTGTCCAAATAGATATTGAATATTGGCGATTTGAGGCCGTAGACCTCATCATTAATCTGTAGGTGTTTTATGGTGACAATAAATAACGCAAGAAAGATTCTACAACGTGTCGACACTCTTCCTCTTTATTTACATGCTTATGCCTTTCATTTAAATATGCGGCTGGAAAGAGTGTTGCCTGCTGA  >  NC_000913/4061030‑4061280

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