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
A1 F1 I1 R1	773	79.9	4112934	92.2%	3792125	104.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,770,404	G→A	234 (TAG→TAA)	yfjR →	CP4‑57 prophage, putative DNA‑binding transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,770,404	0	G	A	100.0%	174.0 / NA	54	234 (TAG→TAA)	yfjR	CP4‑57 prophage, putative DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (25/29); total (25/29)

AGGAGACTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAGCGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACG  >  NC_000913/2770271‑2770522

aGGAGACTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAg                                                                                                                   <  2:134840/139‑1 (MQ=255)

   agaCTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCg                                                                                                                <  1:563913/139‑1 (MQ=255)

       ttttCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCg                                                                                                                <  2:784452/135‑1 (MQ=255)

       ttttCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCg                                                                                                                >  1:784452/1‑135 (MQ=255)

         ttCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTa                                                                                                          >  2:325117/1‑139 (MQ=255)

          tCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTAt                                                                                                         <  2:1018135/139‑1 (MQ=255)

               gcAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAAcc                                                                                                    >  2:931335/1‑139 (MQ=255)

                  aTGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCgg                                                                                                 <  2:561074/139‑1 (MQ=255)

                                 gCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGcc                                                                                  <  1:732979/139‑1 (MQ=255)

                                 gCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGcc                                                                                  >  2:1174666/1‑139 (MQ=255)

                                       ttGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGc                                                                            >  1:646208/1‑139 (MQ=255)

                                        tGAAGCCACGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGcc                                                                           <  1:931335/139‑1 (MQ=255)

                                        tGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGcc                                                                           <  2:508341/139‑1 (MQ=255)

                                        tGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGcc                                                                           <  2:646208/139‑1 (MQ=255)

                                        tGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGcc                                                                           <  1:1174666/139‑1 (MQ=255)

                                            gACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGtt                                                                       >  2:1186633/1‑139 (MQ=255)

                                               ccGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCgg                                                                                                 <  2:44310/110‑1 (MQ=255)

                                               ccGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCgg                                                                                                 >  1:44310/1‑110 (MQ=255)

                                                 ggTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGc                                                                  >  2:170708/1‑139 (MQ=255)

                                                    cTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCAt                                                               <  1:170708/139‑1 (MQ=255)

                                                         ttcaGGCCTTACCCCATTTTCGCTTTATCCAGCATTCCCTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCg                                                          <  1:321078/139‑1 (MQ=255)

                                                             ggCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCAt                                                      >  2:1362320/1‑139 (MQ=255)

                                                                      ccATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTatcat                                             <  2:1446366/139‑1 (MQ=255)

                                                                               cTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGgaggag                                                                                    >  2:1002096/1‑91 (MQ=255)

                                                                               cTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGgaggag                                                                                    <  1:1002096/91‑1 (MQ=255)

                                                                                         cATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGc                                                         <  1:1090077/108‑1 (MQ=255)

                                                                                         cATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGc                                                         >  2:1090077/1‑108 (MQ=255)

                                                                                            tCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAAcc                       >  1:1834391/1‑139 (MQ=255)

                                                                                             cACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCg                      <  2:889017/139‑1 (MQ=255)

                                                                                              aCTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGc                                                                            <  2:1163229/84‑1 (MQ=255)

                                                                                              aCTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGc                                                                            >  1:1163229/1‑84 (MQ=255)

                                                                                              aCTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCAt                                                               <  1:72483/97‑1 (MQ=255)

                                                                                              aCTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCAt                                                               >  2:72483/1‑97 (MQ=255)

                                                                                              aCTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCAt                                                               >  1:405310/1‑97 (MQ=255)

                                                                                              aCTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCAt                                                               <  2:405310/97‑1 (MQ=255)

                                                                                              aCTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTa                                                 <  1:239128/111‑1 (MQ=255)

                                                                                              aCTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTa                                                 >  2:239128/1‑111 (MQ=255)

                                                                                                  cTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCgg                                                                                                 <  2:1943252/59‑1 (MQ=255)

                                                                                                  cTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCgg                                                                                                 >  1:1943252/1‑59 (MQ=255)

                                                                                                   ttACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCa                                                                                                                    >  2:230725/1‑39 (MQ=255)

                                                                                                   ttACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCa                                                                                                                    <  1:230725/39‑1 (MQ=255)

                                                                                                          tGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAg         >  2:840180/1‑139 (MQ=255)

                                                                                                            ttCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGcc                                                                           <  2:1750031/71‑1 (MQ=255)

                                                                                                            ttCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGcc                                                                           >  1:1750031/1‑71 (MQ=255)

                                                                                                               cGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCa    <  1:325117/139‑1 (MQ=255)

                                                                                                                 gCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATggag                                                                                       >  1:152864/1‑54 (MQ=255)

                                                                                                                 gCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATggag                                                                                       <  2:152864/54‑1 (MQ=255)

                                                                                                                 gCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGcc                                                                                  <  2:257398/59‑1 (MQ=255)

                                                                                                                 gCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGcc                                                                                  >  1:257398/1‑59 (MQ=255)

                                                                                                                 gCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCAt                                                      >  1:1664651/1‑87 (MQ=255)

                                                                                                                 gCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCAt                                                      <  2:1664651/87‑1 (MQ=255)

                                                                                                                 gCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGtca                                        <  1:189607/101‑1 (MQ=255)

                                                                                                                 gCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGtca                                        >  2:189607/1‑101 (MQ=255)

                                                                                                                 gCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACg  >  2:1366301/1‑139 (MQ=255)

AGGAGACTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAGCGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACG  >  NC_000913/2770271‑2770522

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A