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
A0 F0 I1 R1	715	38.4	1606192	96.6%	1551581	120.0

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%	138.2 / NA	43	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 (20/23); total (20/23)

AGGAGACTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAGCGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACGGCCCTGACACTTGCAAC  >  NC_000913/2770271‑2770539

aGGAGACTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGTCCACCGGAATAACGCAg                                                                                                                                    <  2:23769/139‑1 (MQ=255)

   agaCTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCg                                                                                                                                 <  1:131365/139‑1 (MQ=255)

   agaCTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCg                                                                                                                                 <  2:418201/139‑1 (MQ=255)

     aCTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCgtt                                                                                                                               <  2:41524/139‑1 (MQ=255)

         ttCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTa                                                                                                                           >  2:82/1‑139 (MQ=255)

                            gtgtCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATggag                                                                                                        <  1:82/139‑1 (MQ=255)

                                   cTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACATCCCAACGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCa                                                                                                 >  1:406610/1‑139 (MQ=255)

                                    tGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACa                                                                                                             <  2:609930/126‑1 (MQ=255)

                                    tGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACa                                                                                                             >  1:609930/1‑126 (MQ=255)

                                                             ggCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCAt                                                                       <  1:255977/139‑1 (MQ=255)

                                                              gCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCa                                                                                                                                     >  1:128493/1‑76 (MQ=255)

                                                              gCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCa                                                                                                                                     <  2:128493/76‑1 (MQ=255)

                                                                   aCCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCgg                                                                                                                  <  2:745648/90‑1 (MQ=255)

                                                                   aCCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCgg                                                                                                                  >  1:745648/1‑90 (MQ=255)

                                                                        aTTTTCGCTTTATCCAGTATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGACGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGGTATTGCCATTATCGCCATTGTTTTCATCg                                                            >  2:499756/1‑139 (MQ=255)

                                                                         ttttCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGt                                                           >  1:569471/1‑139 (MQ=255)

                                                                            tCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGcc                                                                         >  2:572837/1‑122 (MQ=255)

                                                                            tCGCTTTATCCAGCATTCACTGCTTACGTGTGTTCCGGCCGACAGTCCACCGGAATAACGCAGGCGTTGATATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGcc                                                                         <  1:572837/122‑1 (MQ=255)

                                                                               cTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGACATTGTTATCATCGTcatcat                                                     >  2:470626/1‑139 (MQ=255)

                                                                                tttATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCAtt                                                    <  1:318824/139‑1 (MQ=255)

                                                                                     ccAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGaa                                               <  2:615041/139‑1 (MQ=255)

                                                                                            tCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGGCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAAcc                                        >  1:489812/1‑139 (MQ=255)

                                                                                            tCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCg                                                                           >  2:647291/1‑104 (MQ=255)

                                                                                            tCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCg                                                                           <  1:647291/104‑1 (MQ=255)

                                                                                            tCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAAcc                                        >  2:14727/1‑139 (MQ=255)

                                                                                              aCTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCgg                                      >  2:799095/1‑139 (MQ=255)

                                                                                              aCTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCgg                                      >  2:703035/1‑139 (MQ=255)

                                                                                                tGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGcc                                                                                            >  2:621732/1‑83 (MQ=255)

                                                                                                tGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGcc                                                                                            <  1:621732/83‑1 (MQ=255)

                                                                                                    tacttttGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTc                                >  2:211065/5‑139 (MQ=255)

                                                                                                       gTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGa                             <  1:259422/139‑1 (MQ=255)

                                                                                                          tGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAg                          >  1:97004/1‑139 (MQ=255)

                                                                                                            ttCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAAcc                                                                                                                     >  2:414013/1‑46 (MQ=255)

                                                                                                            ttCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAAcc                                                                                                                     <  1:414013/46‑1 (MQ=255)

                                                                                                               cGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCa                     <  2:524632/139‑1 (MQ=255)

                                                                                                               cGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCa                     <  1:799095/139‑1 (MQ=255)

                                                                                                                      cAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCg                                                                           <  1:641235/78‑1 (MQ=255)

                                                                                                                      cAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCg                                                                           >  2:641235/1‑78 (MQ=255)

                                                                                                                       aGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACGGCCCTg             <  1:14727/139‑1 (MQ=255)

                                                                                                                        gCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACGGCCCTGa            <  1:211065/139‑1 (MQ=255)

                                                                                                                        gCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACGGCCCTGa            <  1:703035/139‑1 (MQ=255)

                                                                                                                              cGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACGGCCCTGACACTTg      >  1:62133/1‑139 (MQ=255)

                                                                                                                                  aTAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACGGCCCTGACACTTGCAAc  <  1:106114/139‑1 (MQ=255)

AGGAGACTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAGCGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACGGCCCTGACACTTGCAAC  >  NC_000913/2770271‑2770539

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `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