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 F28 I1 R1	182	57.1	1926220	99.1%	1908884	138.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	684,378	C→T	G12D (GGT→GAT)	rihA ←	pyrimidine‑specific ribonucleoside hydrolase RihA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	684,378	0	C	T	95.8%	152.3 / ‑1.7	48	G12D (GGT→GAT)	rihA	pyrimidine‑specific ribonucleoside hydrolase RihA
Reads supporting (aligned to +/- strand): ref base C (1/1); new base T (20/26); total (21/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.91e-01

ATTAAGCAAGGTCAGCATACGCAGAACATTGCGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGACCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCAGGATGTAACAGATACGAGGGGCGAAACGATAAAGCGTGAGATGGCGCGCAA  >  NC_000913/684242‑684507

aTTAAGCAAGGTCAGCATACGCAGAACATTGCGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTg                                                                                                                                >  1:77363/1‑140 (MQ=255)

     gCAAGGTCAGCATACGCAGAACATTGCGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGTGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCg                                                                                                                           <  1:701669/140‑1 (MQ=255)

      cAAGGTCAGCATACGCAGAACATTGCGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGc                                                                                                                          >  1:225138/1‑140 (MQ=255)

          gTCAGCATACGCAGAACATTGCGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATc                                                                                                                      >  1:509691/1‑140 (MQ=255)

          gTCAGCATACGCAGAACATTGCGTAAGGGTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATc                                                                                                                      >  1:136739/1‑140 (MQ=255)

           tCAGCATACGCAGAACATTGCGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCt                                                                                                                     >  1:258590/1‑140 (MQ=255)

            cAGCATACGCAGAACATTGCGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTa                                                                                                                    <  2:265133/140‑1 (MQ=255)

               cATACGCAGAACATTGCGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGACCTGGGTCGCAATCTAACa                                                                                                                 >  2:430527/1‑140 (MQ=255)

               cATACGCAGAACATTGCGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATA‑CGTCGTCATGATCTGGGTCGCaa                                                                                                                        <  1:914858/132‑1 (MQ=255)

               cATACGCAGAACATTGCGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATA‑CGTCGTCATGATCTGGGTCGCaa                                                                                                                        >  2:914858/1‑132 (MQ=255)

               cATACGCAGAACATTGCGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGGGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACa                                                                                                                 >  2:243850/1‑140 (MQ=255)

                      aGAACATTGCGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGTAGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTgg                                                                                                          <  2:136739/140‑1 (MQ=255)

                      aGAACATTGCGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTgg                                                                                                          <  1:486083/140‑1 (MQ=255)

                      aGAACATTGCGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTgg                                                                                                          <  2:77363/140‑1 (MQ=255)

                      aGAACATTGCGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTgg                                                                                                          <  2:963071/140‑1 (MQ=255)

                       gAACATTGCGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTgg                                                                                                          >  2:381360/1‑139 (MQ=255)

                       gAACATTGCGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTgg                                                                                                          <  1:381360/139‑1 (MQ=255)

                          cATTGCGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGt                                                                                                      >  2:171312/1‑140 (MQ=255)

                           aTTGCGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTg                                                                                                     >  2:170658/1‑140 (MQ=255)

                            ttGCGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGc                                                                                                    <  2:258590/140‑1 (MQ=255)

                              gCGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCa                                                                                                  >  2:811036/1‑140 (MQ=255)

                               cGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCAt                                                                                                 >  2:681062/1‑140 (MQ=255)

                               cGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCAt                                                                                                 >  2:500668/1‑140 (MQ=255)

                                 tAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCAttg                                                                                               <  2:509691/140‑1 (MQ=255)

                                   aGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCAttgtt                                                                                             <  1:170658/140‑1 (MQ=255)

                                                tgtCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGACCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTtgtg                                                                                <  1:430527/140‑1 (MQ=255)

                                                    tGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGct                                                                            <  1:500668/140‑1 (MQ=255)

                                                                    aCGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGt                                                            <  2:89560/140‑1 (MQ=255)

                                                                           tGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCa                                                     <  2:945426/140‑1 (MQ=255)

                                                                           tGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCa                                                     <  2:865145/140‑1 (MQ=255)

                                                                             cTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCAgg                                                   >  2:112844/1‑140 (MQ=255)

                                                                              tttGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCAGGa                                                  <  1:811036/140‑1 (MQ=255)

                                                                               ttGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCAGGAt                                                 <  2:902530/140‑1 (MQ=255)

                                                                                tGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCAGGATg                                                <  1:171312/140‑1 (MQ=255)

                                                                                  aCATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCa                                                     <  2:43123/133‑1 (MQ=255)

                                                                                  aCATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCa                                                     >  1:43123/1‑133 (MQ=255)

                                                                                           tctGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCAGGATGTAACAGATACg                                     <  1:681062/140‑1 (MQ=255)

                                                                                            ctGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCAGGATGTa                                              >  1:936058/1‑130 (MQ=255)

                                                                                            ctGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCAGGATGTa                                              <  2:936058/130‑1 (MQ=255)

                                                                                             tGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCAGGa                                                  >  2:635805/1‑125 (MQ=255)

                                                                                             tGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCAGGa                                                  <  1:635805/125‑1 (MQ=255)

                                                                                                       agggcgagAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCAGGATGTAACAGATACGAGGGGCGa                             >  2:649663/1‑136 (MQ=255)

                                                                                                       agggcgagAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCAGGATGTAACAGATACGAGGGGCGa                             <  1:649663/136‑1 (MQ=255)

                                                                                                         ggcgagAACTATTGCGATAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCAGGATGTAACAGATACGAGGGGCGAAACGAt                       >  2:193839/1‑140 (MQ=255)

                                                                                                                         aTAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCAGGATGTAACAGATACGAGGGGCGAAACGATAAAGCGTGAGATGgcg       <  1:193839/140‑1 (MQ=255)

                                                                                                                         aTAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCAGGATGTAACAGATACGAGGGGCGAAACGATAAAGCGTGAGATGgcg       >  1:376688/1‑140 (MQ=255)

                                                                                                                          tAGCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCAGGATGTAACAGATACGAGGGGCGAAACGATAAAGCGTGAGATGgcgc      <  1:243850/140‑1 (MQ=255)

                                                                                                                            gCGTCGTCATGATCTGGGTCGGAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCAGGATGTAACAGATACGAGGGGCGCAACGATAAAGCGTGAGATGgcgcgc    <  2:742856/140‑1 (MQ=255)

                                                                                                                            gCGTCGTCATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCAGGATGTAACAGATACGAGGGGCGAAACGATAAAGCGTGAGATGgcgcgc    >  2:484047/1‑140 (MQ=255)

                                                                                                                              gtcgtcATGATCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCAGGATGTAACAGATACGAGGGGCGAAACGATAAAGCGTGAGATGGCGCGCaa  <  1:484047/140‑1 (MQ=255)

ATTAAGCAAGGTCAGCATACGCAGAACATTGCGTAAGGTTTTTTCTGGTGTCTGGTTTCCGGCGGAAGACGTAATTGCTTTGACATCAAGCTCTGGTGAGGCGAGGGCGAGAACTATTGCGATAGCGTCGTCATGACCTGGGTCGCAATCTAACAGAATTGGCAGTGCCATTGTTGCTCCTTGTTGTGTGCTTCTTTGCGACAAGGGTAACGCCAGGATGTAACAGATACGAGGGGCGAAACGATAAAGCGTGAGATGGCGCGCAA  >  NC_000913/684242‑684507

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `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