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
A6 F28 I1 R1	191	83.5	2830284	99.3%	2810472	139.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,647,327	T→C	intergenic (‑4/+19)	ydfW ← / ← ydfX	Qin prophage; uncharacterized protein YdfW/Qin prophage; uncharacterized protein YdfX

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,647,327	0	T	C	100.0%	201.4 / NA	55	intergenic (‑4/+19)	ydfW/ydfX	Qin prophage; uncharacterized protein YdfW/Qin prophage; uncharacterized protein YdfX
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (31/24); total (31/24)

CAGGCTTCTTTTTAGGTAACTTCGGGGGCTTAACTTGCTGATGACTTTGCGTTCGGCGCGTAAGCCAGGGATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGTTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGATAGCCTTCCAGCGTTCAAATATCTTCACTCGATTAACGCCAAGCGCT  >  NC_000913/1647194‑1647463

cAGGCTTCTTTTTAGGTAACTTCGGGGGCTTAACTTGCTGATGACTTTGCGTTCGGCGCGTAAGCCAGGGATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATgg                                                                                                                                    <  2:331824/140‑1 (MQ=255)

  ggCTTCTTTTTAGGTAACTTCGGGGGCTTAACTTGCTGATGACTTTGCGTTCGGCGCGTAAGCCAGGGATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGac                                                                                                                                  <  2:598357/140‑1 (MQ=255)

      tcttTTTAGGTAACTTCGGGGGCTTAACTTGCTGATGACTTTGCGTTCGGCGCGTAAGCCAGGGATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACActc                                                                                                                              >  2:382173/1‑140 (MQ=255)

      tcttTTTAGGTAACTTCGGGGGCTTAACTTGCTGATGACTTTGCGTTCGGCGCGTAAGCCAGGGATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACActc                                                                                                                              >  2:1185794/1‑140 (MQ=255)

       cttTTTAGGTAACTTCGGGGGCTTAACTTGCTGATGACTTTGCGTTCGGCGCGTAAGCCAGGGATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACActct                                                                                                                             >  1:1113009/1‑140 (MQ=255)

       cttTTTAGGTAACTTCGGGGGCTTAACTTGCTGATGACTTTGCGTTCGGCGCGTAAGCCAGGGATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACActct                                                                                                                             >  2:602834/1‑140 (MQ=255)

        tttttAGGTAACTTCGGGGGCTTAACTTGCTGATGACTTTGCGTTCGGCGCGTAAGCCAGGGATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCtt                                                                                                                            >  2:1218991/1‑140 (MQ=255)

            tAGGTAACTTCGGGGGCTTAACTTGCTGATGACTTTGCGTTCGGCGCGTAAGCCAGGGATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTtca                                                                                                                        <  1:1336048/140‑1 (MQ=255)

             aGGTAACTTCGGGGGCTTAACTTGCTGATGACTTTGCGTTCGGCGCGTAAGCCAGGGATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTtcat                                                                                                                       <  2:1231843/140‑1 (MQ=255)

                 aaCTTCGGGGGCTTAACTTGCTGATGACTTTGCGTTCGGCGCGTAAGCCAGGGATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCatcatc                                                                                                                   <  2:130252/140‑1 (MQ=255)

                 aaCTTCGGGGGCTTAACTTGCTGATGACTTTGCGTTCGGCGCGTAAGCCAGGGATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCatcatc                                                                                                                   <  1:781225/140‑1 (MQ=255)

                   cTTCGGGGGCTTAACTTGCTGATGACTTTGCGTTCGGCGCGTAAGCCAGGGATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCa                                                                                                                 <  1:1185794/140‑1 (MQ=255)

                        ggggCTTAACTTGCTGATGACTTTGCGTTCGGCGCGTAAGCCAGGGATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGt                                                                                                            <  1:382173/140‑1 (MQ=255)

                                   tGCTGATGACTTTGCGTTCGGCGCGTAAGCCAGGGATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATaa                                                                                                 <  1:467630/140‑1 (MQ=255)

                                      tgatgaCTTTGCGTTCGGCGCGTAAGCCAGGGATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTg                                                                                              <  2:1078892/140‑1 (MQ=255)

                                       gatgaCTTTGCGTTCGGCGCGTAAGCCAGGGATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGc                                                                                             >  2:243877/1‑140 (MQ=255)

                                       gatgaCTTTGCGTTCGGCGCGTAAGCCAGGGATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGc                                                                                             >  2:57681/1‑140 (MQ=255)

                                               tGCGTTCGGCGCGTAAGCCAGGGATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTa                                                                                     >  2:1200612/1‑140 (MQ=255)

                                                                ccAGGGATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCa                                                                    <  2:1293650/140‑1 (MQ=255)

                                                                ccAGGGATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCa                                                                    <  1:1190127/140‑1 (MQ=255)

                                                                    ggATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCt                                                                >  1:1334950/1‑140 (MQ=255)

                                                                         gTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATcc                                                           >  1:1284203/1‑140 (MQ=255)

                                                                         gTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATcc                                                           >  1:1187504/1‑140 (MQ=255)

                                                                         gTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATcc                                                           >  2:1071081/1‑140 (MQ=255)

                                                                         gTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATcc                                                           >  2:1052564/1‑140 (MQ=255)

                                                                         gTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATcc                                                           >  1:564557/1‑140 (MQ=255)

                                                                         gTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATcc                                                           >  1:196568/1‑140 (MQ=255)

                                                                          tCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATccc                                                          >  1:240633/1‑140 (MQ=255)

                                                                            aGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTg                                                        <  1:1218991/140‑1 (MQ=255)

                                                                             gCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTgg                                                       <  1:602834/140‑1 (MQ=255)

                                                                             gCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTgg                                                       <  2:1113009/140‑1 (MQ=255)

                                                                                 tAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTc                                                   <  2:564557/140‑1 (MQ=255)

                                                                                        aaCATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGATAGcc                                            >  2:1270159/1‑140 (MQ=255)

                                                                                        aaCATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGATAGcc                                            >  2:381563/1‑140 (MQ=255)

                                                                                         aCATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGa                                                 <  1:786081/134‑1 (MQ=255)

                                                                                         aCATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGa                                                 >  2:786081/1‑134 (MQ=255)

                                                                                           aTAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGATAGCCTTc                                         <  1:57681/140‑1 (MQ=255)

                                                                                             aGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTg                                                        >  2:1247612/1‑123 (MQ=255)

                                                                                             aGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTg                                                        <  1:1247612/123‑1 (MQ=255)

                                                                                             aGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGATAGCCTTCCa                                       <  2:1334950/140‑1 (MQ=255)

                                                                                             aGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGATAGCCTTCCa                                       >  2:224882/1‑140 (MQ=255)

                                                                                             aGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGATAGCCTTCCa                                       >  2:857763/1‑140 (MQ=255)

                                                                                              gTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGATAGCCTTCCAg                                      >  1:564397/1‑140 (MQ=255)

                                                                                                    tGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGATAGCCTTCCAGCGTTCa                                >  2:1451/1‑140 (MQ=255)

                                                                                                    tGAGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGATAGCCTTCCAGCGTTCa                                >  2:354374/1‑140 (MQ=255)

                                                                                                      aGCGTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGATAGCCTTCCAGCGTTCaaa                              >  2:880180/1‑140 (MQ=255)

                                                                                                         gTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGATAGCCTTCCAGCg                                    >  1:1078052/1‑131 (MQ=255)

                                                                                                         gTAAATCAATACGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGATAGCCTTCCAGCg                                    <  2:1078052/131‑1 (MQ=255)

                                                                                                                   aCGGGCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGATAGCCTTCCAGCGTTCAAATATCTTCACTCGa                 <  1:153241/140‑1 (MQ=255)

                                                                                                                     gggCATTATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGATAGCCTTCCAGCGTTCAAATATCTTCACTCGAtt               >  1:708597/1‑140 (MQ=255)

                                                                                                                          ttATCCACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGATAGCCTTCCAGCGTTCAAATATCTTCACTCGATTAACGc          >  1:813806/1‑140 (MQ=255)

                                                                                                                              ccACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGATAGCCTTCCAGCGTTCAAATATCTTCACTCGATTAACGCCAAg      <  2:915719/140‑1 (MQ=255)

                                                                                                                               cACTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGATAGCCTTCCAGCGTTCAAATATCTTCACTCGATTAACGCCAAgc     <  2:1187504/140‑1 (MQ=255)

                                                                                                                                 cTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGATAGCCTTCCAGCGTTCAAATATCTTCACTCGATTAACGCCAAgcgc   >  2:674555/1‑140 (MQ=255)

                                                                                                                                 cTCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGATAGCCTTCCAGCGTTCAAATATCTTCACTCGATTAACGCCAAgcgc   >  1:1063552/1‑140 (MQ=255)

                                                                                                                                  tCGCTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGATAGCCTTCCAGCGTTCAAATATCTTCACTCGATTAACGCCAAGcgct  <  1:1451/140‑1 (MQ=255)

CAGGCTTCTTTTTAGGTAACTTCGGGGGCTTAACTTGCTGATGACTTTGCGTTCGGCGCGTAAGCCAGGGATGGTCAGCTTTAGGTTTAACATAGTATTTTGAGCGTAAATCAATACGGGCATTATCCACTCGTTCATGGACACTCTTTTCATCATCCAGTGGTAGCCTCCATAATTGCAGGCACTAGCGCCGTGAACTTTTCACGCTTATCCCTGGTGTCGATAGCCTTCCAGCGTTCAAATATCTTCACTCGATTAACGCCAAGCGCT  >  NC_000913/1647194‑1647463

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