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
A5 F28 I1 R1	260	73.5	2514320	99.3%	2496719	138.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,072,883	G→A	A449T (GCG→ACG)	flu →	CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,072,883	0	G	A	100.0%	177.9 / NA	51	A449T (GCG→ACG)	flu	CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (18/33); total (18/33)

GCATTCAGTATCGGAGGCGGTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTCTCACCGGTAACGGC  >  NC_000913/2072748‑2073008

gCATTCAGTATCGGAGGCGGTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACggg                                                                                                                           <  2:647015/140‑1 (MQ=255)

gCATTCAGTATCGGAGGCGGTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACggg                                                                                                                           <  2:702633/140‑1 (MQ=255)

     cAGTATCGGAGGCGGTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGcacca                                                                                                                      <  1:279433/140‑1 (MQ=255)

      aGTATCGGAGGCGGTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGcaccac                                                                                                                     <  2:766738/140‑1 (MQ=255)

        tATCGGAGGCGGTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGcaccacca                                                                                                                   <  2:1191797/140‑1 (MQ=255)

          tCGGAGGCGGTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACg                                                                                                                 >  2:100256/1‑140 (MQ=255)

          tCGGAGGCGGTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACg                                                                                                                 <  2:459214/140‑1 (MQ=255)

                gCGGTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTATTCACCGCCAGGGGCGGCACACTGACggg                                                                                                                           >  1:812703/1‑124 (MQ=255)

                gCGGTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTATTCACCGCCAGGGGCGGCACACTGACggg                                                                                                                           <  2:812703/124‑1 (MQ=255)

                  ggTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATaa                                                                                                         <  1:9488/140‑1 (MQ=255)

                   gTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAAc                                                                                                        >  1:328367/1‑140 (MQ=255)

                    tCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACg                                                                                                       <  2:93989/140‑1 (MQ=255)

                       ggCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGgcg                                                                                                    <  1:355889/140‑1 (MQ=255)

                       ggCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGgcg                                                                                                    <  2:1195355/140‑1 (MQ=255)

                        gCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGgcgc                                                                                                   <  2:668575/140‑1 (MQ=255)

                        gCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGgcgc                                                                                                   <  2:408049/140‑1 (MQ=255)

                        gCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGgcgc                                                                                                   <  2:282969/140‑1 (MQ=255)

                        gCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGgcgc                                                                                                   <  2:842901/140‑1 (MQ=255)

                                 cTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTAc                                                                                          <  1:191402/140‑1 (MQ=255)

                                          gAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCgg                                                                                 >  1:19364/1‑140 (MQ=255)

                                               aGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGa                                                                            >  1:722364/1‑140 (MQ=255)

                                                 gCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACg                                                                          >  2:417529/1‑140 (MQ=255)

                                                    gTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTg                                                                       <  2:173890/140‑1 (MQ=255)

                                                      tcattcaCGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGaa                                                                     <  2:986007/140‑1 (MQ=255)

                                                      tcattcaCGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGaa                                                                     <  1:417529/140‑1 (MQ=255)

                                                               cTGAACGCCGGTGATACGGCCACGGATACCACGGTAAAT‑GCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATAcc                                                           <  1:40713/140‑1 (MQ=255)

                                                                  aaCGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCt                                                         >  2:848611/1‑140 (MQ=255)

                                                                    cGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTATCCTTTCCGGGAAGACGGTGaa                                                                     >  1:837240/1‑126 (MQ=255)

                                                                    cGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGaa                                                                     <  2:837240/126‑1 (MQ=255)

                                                                    cGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGa                                                       <  1:1102520/140‑1 (MQ=255)

                                                                    cGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGa                                                       <  1:1166058/140‑1 (MQ=255)

                                                                      ccGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGAcc                                                     <  2:88897/140‑1 (MQ=255)

                                                                       cGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCa                                                    <  2:127620/140‑1 (MQ=255)

                                                                            aTACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGt                                               >  1:508163/1‑140 (MQ=255)

                                                                                 gCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAgg                                          >  1:1115585/1‑140 (MQ=255)

                                                                                      ggATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATg                                     >  1:950312/1‑140 (MQ=255)

                                                                                      ggATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATg                                     <  2:722364/140‑1 (MQ=255)

                                                                                         tcccACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCAc                                  <  2:490692/138‑1 (MQ=255)

                                                                                         tACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCAc                                  <  1:848611/140‑1 (MQ=255)

                                                                                         tACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCAc                                  <  1:353161/140‑1 (MQ=255)

                                                                                         tACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCAc                                  <  2:420263/140‑1 (MQ=255)

                                                                                                gTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGAGAAGGCGATGCACTCCTGCa                           >  2:238216/1‑140 (MQ=255)

                                                                                                    aTGGCGGACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGa                       <  2:950312/140‑1 (MQ=255)

                                                                                                          gACTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGctct                 >  1:537565/1‑140 (MQ=255)

                                                                                                           aCTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGctctc                >  1:606685/1‑140 (MQ=255)

                                                                                                           aCTGTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGctctc                >  1:663738/1‑140 (MQ=255)

                                                                                                              gTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTCTCa             <  2:508163/140‑1 (MQ=255)

                                                                                                              gTTCACCGCCAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGAGAAGGCGATGCACTCCTGCAGGGAGGCTCTCTCa             <  1:238216/140‑1 (MQ=255)

                                                                                                                       cAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTCTCACCGGTAACg    >  1:476159/1‑140 (MQ=255)

                                                                                                                       cAGGGGCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTCTCACCGGTAACg    >  1:57074/1‑140 (MQ=255)

                                                                                                                         ggggCGGCACACTGACGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTCTCACCGGTAACGGc  >  1:785435/1‑140 (MQ=255)

GCATTCAGTATCGGAGGCGGTCAGGCGGATGCCCTGATGCTGGAAAAAGGCAGTTCATTCACGCTGAACGCCGGTGATACGGCCACGGATACCACGGTAAATGGCGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTCTCACCGGTAACGGC  >  NC_000913/2072748‑2073008

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A