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
A1 F28 I1 R1	163	52.9	1786516	99.3%	1774010	139.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,908,414	A→G	intergenic (‑48/+135)	pstB ← / ← pstA	phosphate ABC transporter ATP binding subunit/phosphate ABC transporter membrane subunit PstA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,908,414	0	A	G	97.9%	160.4 / NA	48	intergenic (‑48/+135)	pstB/pstA	phosphate ABC transporter ATP binding subunit/phosphate ABC transporter membrane subunit PstA
Reads supporting (aligned to +/- strand): ref base A (1/0); new base G (27/20); total (28/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGTTTTTCAGGGCATGGAATTTGCCGTAGTAGAAGTTCAAATTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTACCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTACAGAGTCAAAAAGGCGCTCGGTCGGTCCCCTCGCCCCTCTGGGGAGAGGGTTAGGGTGAGGGGAAAACCGTGTCAGCA  >  NC_000913/3908282‑3908545

tGTTTTTCAGGGCATGGAATTTGCCGTAGTAGAAGTTCAAATTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAgg                                                                                                                              >  1:153666/1‑140 (MQ=255)

tGTTTTTCAGGGCATGGAATTTGCCGTAGTAGAAGTTCAAATTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAgg                                                                                                                              >  2:813051/1‑140 (MQ=255)

tGTTTTTCAGGGCATGGAATTTGCCGTAGTAGAAGTTCAAATTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAgg                                                                                                                              >  2:759947/1‑140 (MQ=255)

     ttCAGGGCATGGAATTTGCCGTAGTAGAAGTTCAAATTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGa                                                                                                                         >  1:838830/1‑140 (MQ=255)

            cATGGAATTTGCCGTAGTAGAAGTTCAAATTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCgg                                                                                                                          >  2:856816/1‑132 (MQ=255)

            cATGGAATTTGCCGTAGTAGAAGTTCAAATTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCgg                                                                                                                          <  1:856816/132‑1 (MQ=255)

              tGGAATTTGCCGTAGTAGAAGTTCAAATTACGAACCTGAATTTTACTCGGGGCAGCTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTACCGTAGGCCGGATCAGGCGtt                                                                                                                >  1:788640/1‑140 (MQ=255)

               ggAATTTGCCGTAGTAGAAGTTCAAATTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTc                                                                                                               >  1:281528/1‑140 (MQ=255)

               ggAATTTGCCGTAGTAGAAGTTCAAATTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTc                                                                                                               >  1:712636/1‑140 (MQ=255)

                     tGCCGTAGTAGAAGTTCAAATTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCAcgccg                                                                                                         >  2:500613/1‑140 (MQ=255)

                     tGCCGTAGTAGAAGTTCAAATTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCAcgccg                                                                                                         >  1:432152/1‑140 (MQ=255)

                           agtagAAGTTCAAATTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCg                                                                                                   >  1:810701/1‑140 (MQ=255)

                           agtagAAGTTCAAATTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCg                                                                                                   >  2:175100/1‑140 (MQ=255)

                             tagAAGTTCAAATTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGc                                                                                                 <  2:153666/140‑1 (MQ=255)

                               gAAGTTCAAATTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCaa                                                                                               <  1:500613/140‑1 (MQ=255)

                               gAAGTTCAAATTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCaa                                                                                               <  1:759947/140‑1 (MQ=255)

                               gAAGTTCAAATTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATACGGCaa                                                                                               <  1:334177/140‑1 (MQ=255)

                                    tCAAATTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAgtgt                                                                                          <  2:883717/140‑1 (MQ=255)

                                    tCAAATTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAgtgt                                                                                          <  2:432152/140‑1 (MQ=255)

                                      aaaTTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAgtgt                                                                                          <  2:479100/138‑1 (MQ=255)

                                      aaaTTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAgtgt                                                                                          >  1:479100/1‑138 (MQ=255)

                                      aaaTTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTa                                                                                        <  1:175100/140‑1 (MQ=255)

                                         ttACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAAcc                                                                                     >  1:484859/1‑140 (MQ=255)

                                             gAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCgtgt                                                                                 >  1:490402/1‑140 (MQ=255)

                                              aaCCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTa                                                                                <  1:743104/140‑1 (MQ=255)

                                              aaCCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTa                                                                                <  1:813051/140‑1 (MQ=255)

                                                ccTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCCTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAAcc                                                                                     >  1:297472/1‑133 (MQ=255)

                                                ccTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCCTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAAcc                                                                                     <  2:297472/133‑1 (MQ=255)

                                                  tGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTACaga                                                                            <  1:143376/140‑1 (MQ=255)

                                                      ttttACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTaa                                                                                       <  1:636367/125‑1 (MQ=255)

                                                      ttttACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTaa                                                                                       >  2:636367/1‑125 (MQ=255)

                                                                     tttCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTACAGAGTCAAAAAGGCGCtcggtc                                                         <  2:838830/140‑1 (MQ=255)

                                                                             aTACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTACAGAGTCAAAAAGGCGCTCGGTCGGTCCCCt                                                 <  2:656746/140‑1 (MQ=255)

                                                                               aCTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTACAGAGTC‑AAAAGGCGCTCGGTCGGTCCCCTCg                                               <  1:30729/139‑1 (MQ=255)

                                                                               aCTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTACAGAGTC‑AAAAGGCGCTCGGTCGGTCCCCTCg                                               >  2:30729/1‑139 (MQ=255)

                                                                                     tGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTACAGAGTCAAAAAGGCGCTCGGTCGGTCCCCTCGCCCctc                                         >  2:151275/1‑140 (MQ=255)

                                                                                     tGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTACAGAGTCAAAAAGGCGCTCGGTCGGTCCCCTCGCCCctc                                         >  2:327934/1‑140 (MQ=255)

                                                                                     tGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTACAGAGTCAAAAAGGCGCTCGGTCGGTCCCCTCGCCCctc                                         >  1:736502/1‑140 (MQ=255)

                                                                                           cTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTACAGAGTCAAAAAGGCGCTCGGTCGGTCCCCTCGCCCCTCTGGGga                                   <  1:741064/140‑1 (MQ=255)

                                                                                             tttCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTACAGAGTCAAAAAGGCGCTCGGTCGGTCCCCTCGCCCCTCTGGGgaga                                 <  1:449964/140‑1 (MQ=255)

                                                                                             tttCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTACAGAGTCAAAAAGGCGCTCGGTCGGTCCCCTCGCCCCTCTGGGgaga                                 >  1:786723/1‑140 (MQ=255)

                                                                                                 cTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTACAGAGTCAAAAAGGCGCTCGGTCGGTCCCCTCGCCCCTCTGGGGAGAGGGt                             <  1:685721/140‑1 (MQ=255)

                                                                                                      cGTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTACAGAGTCAAAAAGGCGCTCGGTCGGTCCCCTCGCCCCTCTGGGGAGAGGGTTAggg                        >  2:285293/1‑140 (MQ=255)

                                                                                                       gTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTACAGAGTCAAAAAGGCGCTCGGTCGGTCCCCTCGCCCCTCTGGGGAGAGGGTTAGGGt                       <  2:490402/140‑1 (MQ=255)

                                                                                                       gTGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTACAGAGTCAAAAAGGCGCTCGGTCGGTCCCCTCGCCCCTCTGGGGAGAGGGTTAGGGt                       <  2:786723/140‑1 (MQ=255)

                                                                                                        tGCCTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTACAGAGTCAAAAAGGCGCTCGGTCGGTCCCCTCGCCCCTCTGGGGAGAGGGTTAGGGTg                      >  1:456274/1‑140 (MQ=255)

                                                                                                          ccTGATGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTACAGAGTCAAAAAGGCGCTCGGTCGGTCCCCTCGCCCCTCTGGGGAGAGGGTTAGGGTGAg                    >  1:497798/1‑140 (MQ=255)

                                                                                                               tGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTACAGAGTCAAAAAGGCGCTCGGTCGGTCCCCTCGCCCCTCTGGGGAGAGGGTTAGGGTGAGGGGaa               >  2:704330/1‑140 (MQ=255)

                                                                                                               tGCACTTCGCTAATCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTACAGAGTCAAAAAGGCGCTCGGTCGGTCCCCTCGCCCCTCTGGGGAGAGGGTTAGGGTGAGGGGaa               >  1:720589/1‑140 (MQ=255)

                                                                                                                            tCAGGCTTGCCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTACAGAGTCAAAAAGGCGCTCGGTCGGTCCCCTCGCCCCTCTGGGGAGAGGGTTAGGGTGAGGGGAAAACCGTGTCAGCa  >  2:349067/1‑140 (MQ=255)

TGTTTTTCAGGGCATGGAATTTGCCGTAGTAGAAGTTCAAATTACGAACCTGAATTTTACTCGGGGCAGTTTCAACCATACTCATTGCAATCTTTTCCTCATCGTGCCTGATGCACTTCGCTAATCAGGCTTACCGTAGGCCGGATCAGGCGTTCACGCCGCATCCGGCAAAGTGTTAACCGTGTACAGAGTCAAAAAGGCGCTCGGTCGGTCCCCTCGCCCCTCTGGGGAGAGGGTTAGGGTGAGGGGAAAACCGTGTCAGCA  >  NC_000913/3908282‑3908545

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A