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
A10 F28 I1 R1	180	66.5	2263572	99.4%	2249990	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,104,287	G→A	L65L (CTG→CTA)	yggX →	putative Fe(2(+))‑trafficking protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,104,287	0	G	A	97.8%	155.5 / NA	46	L65L (CTG→CTA)	yggX	putative Fe(2(+))‑trafficking protein
Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (26/19); total (26/20)
Fisher's exact test for biased strand distribution p-value = 4.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TACCCCGGCGAGCTGGGAAAACGCATCTATAACGAGATCTCCAAAGAAGCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTGCTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATCGAGGGCTATACGCCGGAAGATAAAAAATAAAAACAGTGCCGGAGCACGCCTCCGGCAACTTGCATAAAAACAAACACAACACG  >  NC_000913/3104156‑3104421

tACCCCGGCGAGCTGGGAAAACGCATCTATAACGAGATCTCCAAAGAAGCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCa                                                                                                                                >  2:1015171/1‑140 (MQ=255)

     cGGCGAGCTGGGAAAACGCATCTATAACGAGATCTCCAAAGAAGCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGgaga                                                                                                                           >  2:698831/1‑140 (MQ=255)

          aGCTGGGAAAACGCATCTATAACGAGATCTCCAAAGAAGCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTc                                                                                                                      >  1:698595/1‑140 (MQ=255)

            cTGGGAAAACGCATCTATAACGAGATCTCCAAAGAAGCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCaa                                                                                                                    >  2:17909/1‑140 (MQ=255)

             tGGGAAAACGCATCTATAACGAGATCTCCAAAGAAGCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAAc                                                                                                                   >  2:703938/1‑140 (MQ=255)

                      gCATCTATAACGAGATCTCCAAAGAAGCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTc                                                                                                          <  1:1015171/140‑1 (MQ=255)

                         tCTATAACGAGATCTCCAAAGAAGCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGtt                                                                                                           <  2:338785/136‑1 (MQ=255)

                         tCTATAACGAGATCTCCAAAGAAGCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGtt                                                                                                           >  1:338785/1‑136 (MQ=255)

                         tCTATAACGAGATCTCCAAAGAAGCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAg                                                                                                       >  2:1068653/1‑140 (MQ=255)

                          cTATAACGAGATCTCCAAAGAAGCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCTCCGCAAGCTGCTTGAGCAGGAGATGGTCAGCTTCCTGTTCGAgg                                                                                                      <  1:698831/140‑1 (MQ=255)

                               aCGAGATCTCCAAAGAAGCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTaaa                                                                                                 <  1:1042953/140‑1 (MQ=255)

                               aCGAGATCTCCAAAGAAGCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTaaa                                                                                                 <  1:783752/140‑1 (MQ=255)

                               aCGAGATCTCCAAAGAAGCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTaaa                                                                                                 <  1:1068653/140‑1 (MQ=255)

                                 gagaTCTCCAAAGAAGCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAaga                                                                                               <  1:427865/140‑1 (MQ=255)

                                  agaTCTCCAAAGAAGCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAagag                                                                                              >  1:911387/1‑140 (MQ=255)

                                    aTCTCCAAAGAAGCCTGGGCGCAGTTGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGt                                                                                            <  1:725367/140‑1 (MQ=255)

                                    aTCTCCAAAGAAGCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGtt                                                                                                           <  1:499640/125‑1 (MQ=255)

                                    aTCTCCAAAGAAGCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGtt                                                                                                           >  2:499640/1‑125 (MQ=255)

                                      ctcCAAAGAAGCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGc                                                                                          >  2:366506/1‑140 (MQ=255)

                                      ctcCAAAGAAGCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGc                                                                                          <  1:17909/140‑1 (MQ=255)

                                      ctcCAAAGAAGCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGc                                                                                          >  1:753899/1‑140 (MQ=255)

                                           aagaagCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGc                                                                                          <  1:134492/135‑1 (MQ=255)

                                           aagaagCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGc                                                                                          >  2:134492/1‑135 (MQ=255)

                                           aagaagCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATc                                                                                     <  2:728902/140‑1 (MQ=255)

                                           aagaagCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATc                                                                                     <  2:911387/140‑1 (MQ=255)

                                             gaagCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATCGa                                                                                   <  2:698595/140‑1 (MQ=255)

                                              aagCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATCGAg                                                                                  >  1:74526/1‑140 (MQ=255)

                                                 ccTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATCGAGGGc                                                                               >  1:722373/1‑140 (MQ=255)

                                                 ccTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATAAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATCGAGGGc                                                                               >  2:1010953/1‑140 (MQ=255)

                                                  cctggCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATCGAGGGCt                                                                              >  2:936400/4‑140 (MQ=255)

                                                  cTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATAATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGATAAAGAGGTGCATATCGAGGGCt                                                                              <  1:344719/140‑1 (MQ=255)

                                                     ggCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATCGAGGGCtata                                                                           <  1:703938/140‑1 (MQ=255)

                                                          aGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATCGAGGGCTATACGCCg                                                                      >  2:417489/1‑140 (MQ=255)

                                                          aGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATCGAGGGCTATACGCCg                                                                      >  2:692771/1‑140 (MQ=255)

                                                                      aGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATCGAGGGCTATACGCCGGAAGataaaaaa                                                          >  2:337525/1‑140 (MQ=255)

                                                                      aGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATCGAGGGCTATACGCCGGAAGataaaaaa                                                          >  2:517701/1‑140 (MQ=255)

                                                                           aCCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATCGAGGGCTATACGCCGGAAGataaaaaataaaa                                                     >  1:127590/1‑140 (MQ=255)

                                                                               tGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATCGAGGGCTATACGCCGGAAGATAAAAAATAAAAACAg                                                 >  2:276914/1‑140 (MQ=255)

                                                                               tGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATCGAGGGCTATACGCCGGAAGATAAAAAATAAAAACAg                                                 >  1:886947/1‑140 (MQ=255)

                                                                                      tAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATCGAGGGCTATACGCCGGAAGATAAAAAATAAAAACAGTGCCGGa                                          >  1:559229/1‑140 (MQ=255)

                                                                                         tGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATCGAGGGCTATACGCCGGAAGATAAAAAATAAAAACAGTGCCGGAGCa                                       <  1:276914/140‑1 (MQ=255)

                                                                                                           gatgaATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATCGAGGGCTATACGCCGGAAGATAAAAAATAAAAACAGTGCCGGAGCACGCCTCCGGCAACTTGCa                     <  1:517701/140‑1 (MQ=255)

                                                                                                            atgaATGCCGAGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATCGAGGGCTATACGCCGGAAGATAAAAAATAAAAACAGTGCCGGAGCACGCCTCCGGCAACTTGCAt                    >  2:515571/1‑140 (MQ=255)

                                                                                                                      aGCACCGCAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATCGAGGGCTATACGCCGGAAGATAAAAAATAAAAACAGTGCCGGAGCACGCCTCCGGCAACTTGCATAGaaacaaac          <  1:1065332/140‑1 (MQ=255)

                                                                                                                             cAAGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATCGAGGGCTATACGCCGGAAGATAAAAAATAAAAACAGTGCCGGAGCACGCCTCCGGCAACTTGCATAAAAACAaacacaacac   >  2:852490/1‑140 (MQ=255)

                                                                                                                              aaGCTACTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATCGAGGGCTATACGCCGGAAGATAAAAAATAAAAACAGTGCCGGAGCACGCCTCCGGCAACTTGCATAAAAACAAACACAACACg  <  1:337525/140‑1 (MQ=255)

TACCCCGGCGAGCTGGGAAAACGCATCTATAACGAGATCTCCAAAGAAGCCTGGGCGCAGTGGCAGCACAAGCAAACCATGCTGATTAATGAAAAGAAACTCAACATGATGAATGCCGAGCACCGCAAGCTGCTTGAGCAGGAGATGGTCAACTTCCTGTTCGAGGGTAAAGAGGTGCATATCGAGGGCTATACGCCGGAAGATAAAAAATAAAAACAGTGCCGGAGCACGCCTCCGGCAACTTGCATAAAAACAAACACAACACG  >  NC_000913/3104156‑3104421

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