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
A8 F1 I1 R1	82	28.6	1225488	97.4%	1193625	116.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,548,789	A→G	intergenic (+1/‑19)	fimG → / → fimH	minor component of type 1 fimbriae/minor component of type 1 fimbriae

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,548,789	0	A	G	100.0%	206.1 / NA	55	intergenic (+1/‑19)	fimG/fimH	minor component of type 1 fimbriae/minor component of type 1 fimbriae
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (27/28); total (27/28)

TTCAGGTGGATGATTCCTCACAATCAGCGCACTTCCCGTTACAGGTCAGAGCATTGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCC  >  NC_000913/4548664‑4548924

ttCAGGTGGATGATTCCTCACAATCAGCGCACTTCCCGTTACAGGTCAGAGCATTGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAgatga                                                                                                                            >  1:201983/1‑139 (MQ=255)

             ttCCTCACAATCAGCGCACTTCCCGTTACAGGTCAGAGCATTGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACg                                                                                                               <  2:105925/139‑1 (MQ=255)

               ccTCACAATCAGCGCACTTCCCGTTACAGGTCAGAGCATTGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAg                                                                                                             >  2:251687/1‑139 (MQ=255)

                      aTCAGCGCACTTCCCGTTACAGGTCAGAGCATTGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTAc                                                                                                      <  1:215461/139‑1 (MQ=255)

                         aGCGCACTTCCCGTTACAGGTCAGAGCATTGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCt                                                                                                   <  2:464482/139‑1 (MQ=255)

                         aGCGCACTTCCCGTTACAGGTCAGAGCATTGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCt                                                                                                   <  1:151597/139‑1 (MQ=255)

                         aGCGCACTTCCCGTTACAGGTCAGAGCATTGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCt                                                                                                   <  1:170908/139‑1 (MQ=255)

                          gcgcACTTCCCGTTACAGGTCAGAGCATTGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAAt                                                                                                                     <  1:396643/120‑1 (MQ=255)

                          gcgcACTTCCCGTTACAGGTCAGAGCATTGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAAt                                                                                                                     >  2:396643/1‑120 (MQ=255)

                           cgcACTTCCCGTTACAGGTCAGAGCATTGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGt                                                                                                 >  1:235344/1‑139 (MQ=255)

                                ttCCCGTTACAGGTCAGAGCATTGACAGTAAGTGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGCTTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCt                                                                                            <  2:115308/139‑1 (MQ=255)

                                 tCCCGTTACAGGTCAGAGCATTGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTg                                                                                           <  2:291830/139‑1 (MQ=255)

                                   ccGTTACAGGTCAGAGCATTGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACg                                                                                                               >  2:151892/1‑117 (MQ=255)

                                   ccGTTACAGGTCAGAGCATTGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACg                                                                                                               <  1:151892/117‑1 (MQ=255)

                                            gTCAGAGCATTGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATg                                                                                >  1:190021/1‑139 (MQ=255)

                                            gTCAGAGCATTGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATg                                                                                >  2:587883/1‑139 (MQ=255)

                                                 agCATTGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTg                                                                           <  1:107040/139‑1 (MQ=255)

                                                 agCATTGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTg                                                                           >  2:348803/1‑139 (MQ=255)

                                                   cATTGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGt                                                                         <  2:200898/139‑1 (MQ=255)

                                                      tGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGc                                                                             <  2:250363/132‑1 (MQ=255)

                                                      tGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGc                                                                             >  1:250363/1‑132 (MQ=255)

                                                      tGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCgg                                                                      >  1:538683/1‑139 (MQ=255)

                                                      tGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCgg                                                                      >  2:13998/1‑139 (MQ=255)

                                                      tGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCgg                                                                      >  1:145767/1‑139 (MQ=255)

                                                        aCAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAagag                                                                                                                                <  1:378549/79‑1 (MQ=255)

                                                        aCAGTAAATGGCGGAGCCACTCAGGGAAACATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAagag                                                                                                                                >  2:378549/1‑79 (MQ=255)

                                                            tAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATg                                                                <  1:556507/139‑1 (MQ=255)

                                                             aaaTGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGt                                                                                          >  2:81393/1‑112 (MQ=255)

                                                             aaaTGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGt                                                                                          <  1:81393/112‑1 (MQ=255)

                                                               aTGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACTAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCt                                                             >  2:386780/1‑139 (MQ=255)

                                                                      aGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAagag                                                                                                                                >  2:554015/1‑65 (MQ=255)

                                                                      aGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAagag                                                                                                                                <  1:554015/65‑1 (MQ=255)

                                                                      aGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCAtt                                                      >  1:148417/1‑139 (MQ=255)

                                                                                     cATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTg                                                                                              <  2:549546/84‑1 (MQ=255)

                                                                                     cATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTg                                                                                              >  1:549546/1‑84 (MQ=255)

                                                                                     cATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCATTCGCCTGTAAAACCGc                                       >  2:260995/1‑139 (MQ=255)

                                                                                      aTTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAgatga                                                                                                                            <  1:81170/53‑1 (MQ=255)

                                                                                      aTTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAgatga                                                                                                                            >  2:81170/1‑53 (MQ=255)

                                                                                          aGGCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATg                                  <  1:13998/139‑1 (MQ=255)

                                                                                           ggCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATgg                                 <  2:235344/139‑1 (MQ=255)

                                                                                           ggCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATgg                                 <  1:287720/139‑1 (MQ=255)

                                                                                           ggCAGTGATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGT‑ATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGt                                <  2:201983/139‑1 (MQ=255)

                                                                                                 gATTAGCATCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGc                           >  2:155107/1‑139 (MQ=255)

                                                                                                         tCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTa                   <  1:260995/139‑1 (MQ=255)

                                                                                                         tCACCTATACCTACAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTa                   <  2:148417/139‑1 (MQ=255)

                                                                                                                     aCAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCa       >  2:542941/1‑139 (MQ=255)

                                                                                                                      cAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCg                            <  1:546340/117‑1 (MQ=255)

                                                                                                                      cAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCg                            >  2:546340/1‑117 (MQ=255)

                                                                                                                      cAGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAg      <  1:348803/139‑1 (MQ=255)

                                                                                                                       aGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATg                                  <  1:123188/110‑1 (MQ=255)

                                                                                                                       aGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATg                                  >  2:123188/1‑110 (MQ=255)

                                                                                                                       aGCTGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAgc     >  1:504066/1‑139 (MQ=255)

                                                                                                                          tGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCAtt                                                      >  1:319590/1‑87 (MQ=255)

                                                                                                                          tGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCAtt                                                      <  2:319590/87‑1 (MQ=255)

                                                                                                                          tGAGCCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGcc  >  2:606925/1‑139 (MQ=255)

TTCAGGTGGATGATTCCTCACAATCAGCGCACTTCCCGTTACAGGTCAGAGCATTGACAGTAAATGGCGGAGCCACTCAGGGAACCATTCAGGCAGTGATTAGCATCACCTATACCTACAGCTGAACCCGAAGAGATGATTGTAATGAAACGAGTTATTACCCTGTTTGCTGTACTGCTGATGGGCTGGTCGGTAAATGCCTGGTCATTCGCCTGTAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCC  >  NC_000913/4548664‑4548924

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