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
A21 F12 I1 R1	17	33.0	1187876	93.7%	1113039	142.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	4,110,744	G→T	intergenic (+59/+787)	cdh → / ← yiiQ	CDP‑diacylglycerol phosphotidylhydrolase/DUF1454 family putative periplasmic protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	4,110,744	0	G	T	97.6%	117.4 / ‑3.6	42	intergenic (+59/+787)	cdh/yiiQ	CDP‑diacylglycerol phosphotidylhydrolase/DUF1454 family putative periplasmic protein
Reads supporting (aligned to +/- strand): ref base G (0/1); new base T (20/21); total (20/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.12e-01

TTGCTGGCGACACAACGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATACCCGC  >  NC_000913_3_pae_tpiA/4110599‑4110886

ttGCCGGCGACACTACGAAATTTACTGTCGTTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAtgcgg                                                                                                                                            <  1:205654/150‑1 (MQ=255)

   cTGGCGACACAACGAAATCTCCTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGgcc                                                                                                                                         >  1:589696/1‑150 (MQ=255)

    tGGCGACACAACGAATTCTACTGTCGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGcccc                                                                                                                                        <  1:541709/150‑1 (MQ=255)

             aaacaattCTACTGACGATTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCAGCCCCGCCGCGAGc                                                                                                                               >  2:132479/8‑150 (MQ=255)

                   tacTACGGAGGCTACACCGTGCTTGAGCAGAGGAAATCCAGTATTATCAGTGTGATGTTTGGCGTGAAGGCGAAGAGTTAAGGAAATTAAGTGCCGGCTATGAAAGTCGGCACCTGTCAGACTTCATGCGGCTCCGACGCGAGCGGGTTc                                                                                                                         <  2:74028/148‑1 (MQ=255)

                       acggACTCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCAGCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCa                                                                                                                     <  1:520032/147‑1 (MQ=255)

                          ggcGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAAtt                                                                                                                  <  1:149655/148‑1 (MQ=255)

                          gACGCTTAACCGTGCTCCAGTCGGGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAAtt                                                                                                                  <  2:468704/150‑1 (MQ=255)

                             gCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGGTTCGCCAATTCTa                                                                                                               >  1:43448/1‑150 (MQ=255)

                              cTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTaa                                                                                                              >  2:12170/1‑150 (MQ=255)

                                  aCCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATc                                                                                                          >  1:453481/1‑150 (MQ=255)

                                     gTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTa                                                                                                       <  1:150911/150‑1 (MQ=255)

                                      tGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTac                                                                                                      >  2:419810/1‑149 (MQ=255)

                                      tGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGAGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTaa                                                                                                      <  2:508187/150‑1 (MQ=255)

                                        cTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGa                                                                                                    <  1:364182/150‑1 (MQ=255)

                                          tgaGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGAGTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGata                                                                                                  <  2:262871/148‑1 (MQ=255)

                                               cGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGCTTCGCCAATTCTAAGATCTTCAGATATGGGt                                                                                             >  2:194259/1‑150 (MQ=255)

                                                       ttCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGCACTCCGACTCCTTTAAGCCACAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGcc                                                                                     <  1:141798/150‑1 (MQ=255)

                                                                 tcaGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCCCGGCTg                                                                           >  1:303831/1‑150 (MQ=255)

                                                                     tgtgAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCt                                                                       >  1:91609/1‑150 (MQ=255)

                                                                      gtgAGATTTTGCGTTAAGGCGAAGAATTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCtt                                                                      <  1:482444/150‑1 (MQ=255)

                                                                       tgAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTg                                                                     >  1:102603/1‑150 (MQ=255)

                                                                       tgAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGACGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTACGATCTTACGCTCTGGGTCTTTTGCCTTCACGGCCGCGCTTg                                                                     >  2:21603/1‑150 (MQ=255)

                                                                          gaTTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCa                                                                  <  1:6987/150‑1 (MQ=255)

                                                                                gCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAaca                                                            <  1:143359/150‑1 (MQ=255)

                                                                                     aaGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCCAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTcca                                                       >  2:148436/1‑149 (MQ=255)

                                                                                             gagTTAAGGAACGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGACCTTACCAGATGTGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGcc                                               <  1:560998/150‑1 (MQ=255)

                                                                                                       aagtaagtGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAgc                                     <  2:21709/150‑1 (MQ=255)

                                                                                                          taagtGCCGGATATGAAATCCGGGACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGTAACACTCCCCTCGTGCCGAGTTTAAGcgcg                                  <  2:361828/150‑1 (MQ=255)

                                                                                                          taagtGCCGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGcgcg                                  >  1:436506/1‑150 (MQ=255)

                                                                                                              tGCCGGATTTCATATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCa                                                                  >  1:292505/1‑114 (MQ=255)

                                                                                                              tGCCGGATTTCATATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCa                                                                  <  2:292505/114‑1 (MQ=255)

                                                                                                                ccGGATATGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCa                            >  2:496397/1‑150 (MQ=255)

                                                                                                                       tGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCtt                                                                      <  1:108886/101‑1 (MQ=255)

                                                                                                                       tGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCtt                                                                      >  2:108886/1‑101 (MQ=255)

                                                                                                                       tGAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCct                     >  1:164462/1‑150 (MQ=255)

                                                                                                                        gAAATCCGGCACCTGTCAGACTTAATGCGGCCCCGCCGGGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCctc                    <  2:190534/150‑1 (MQ=255)

                                                                                                                               ggCACCTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGctc             <  1:7666/150‑1 (MQ=255)

                                                                                                                                    cTGTCAGACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAAt        >  1:533550/1‑150 (MQ=255)

                                                                                                                                          gACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATACCCGc  <  1:338460/150‑1 (MQ=255)

                                                                                                                                          gACTTAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGGTTAAGCGCGGCTTCTACGTGCTCTCCGCTTTCAATGCCCGc  >  2:495751/1‑150 (MQ=255)

                                                                                                                                             ttAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCt                                                                                    <  1:78215/65‑1 (MQ=255)

                                                                                                                                             ttAATGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCt                                                                                    >  2:78215/1‑65 (MQ=255)

TTGCTGGCGACACAACGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATACCCGC  >  NC_000913_3_pae_tpiA/4110599‑4110886

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A