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
A3 F44 I0 R1	64	42.0	921266	98.7%	909289	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,373,531	G→T	13.6%	A82E (GCG→GAG)	pbuG ←	Guanine/hypoxanthine permease PbuG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,373,531	0	G	T	13.6%	156.8 / 12.1	50	A82E (GCG→GAG)	pbuG	Guanine/hypoxanthine permease PbuG
Reads supporting (aligned to +/- strand): ref base G (25/18); new base T (3/4); total (28/22)
Fisher's exact test for biased strand distribution p-value = 6.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.69e-01

CCCTAAACCCTGTGACGGTTAATATCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAAC  >  USA300TCH1516_ALE/2373391‑2373664

cccTAAACCCTGTGACGGTTAATATCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAAGACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACg                                                                                                                                       >  2:358192/1‑141 (MQ=255)

 ccTAAACCCTGTGACGGTTAATATCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGc                                                                                                                                      >  2:352213/1‑141 (MQ=255)

 ccTAAACCCTGTGACGGTTAATATCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGCTAACACAACAGTAAATGCAAAGAATGCGTTTAATCCCATACCTGGTGCTAACGc                                                                                                                                      >  2:365261/1‑141 (MQ=255)

  cTAAACCCTGTGACGGTTAATATCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCa                                                                                                                                     >  1:14959/1‑141 (MQ=255)

  cTAAACCCTGTGACGGTTAATATCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCa                                                                                                                                     >  2:357919/1‑141 (MQ=255)

  cTAAACCCTGTGACGGTTAATATCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCa                                                                                                                                     >  1:392035/1‑141 (MQ=255)

    aaaCCCTGTGACGGTTAATATCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAAt                                                                                                                                   >  1:303096/1‑141 (MQ=255)

              aCGGTTAATATCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACTCAATTGGATATTTa                                                                                                                         >  1:237936/1‑141 (MQ=255)

              aCGGTTAATATCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACTCAATTGGATATTTa                                                                                                                         >  1:238086/1‑141 (MQ=255)

              aCGGTTAATATCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACTCAATTGGATATTTa                                                                                                                         >  1:322371/1‑141 (MQ=255)

              aCGGTTAATATCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATCGGATATTTa                                                                                                                         >  2:42226/1‑141 (MQ=255)

                 gTTAATATCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACTCAATTGGATATTTAGCt                                                                                                                      <  2:445395/141‑1 (MQ=255)

                 gTTAATATCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCt                                                                                                                      <  2:262062/141‑1 (MQ=255)

                 gTTAATATCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCt                                                                                                                      <  2:64742/141‑1 (MQ=255)

                      tatCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAg                                                                                                                 >  2:82391/1‑141 (MQ=255)

                      tatCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAg                                                                                                                 >  2:26595/1‑141 (MQ=255)

                              aGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGa                                                                                                         <  1:360648/141‑1 (MQ=255)

                                      ccTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAg                                                                                                 <  1:223477/141‑1 (MQ=255)

                                           gaATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTAc                                                                                            <  2:152894/141‑1 (MQ=255)

                                                 aaCGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAAtgc                                                                                      >  2:184214/1‑141 (MQ=255)

                                                 aaCGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAAtgc                                                                                      >  2:93151/1‑141 (MQ=255)

                                                 aaCGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAAtgc                                                                                      >  2:282763/1‑141 (MQ=255)

                                                           aaaCCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCa                                                                            >  2:253417/1‑141 (MQ=255)

                                                           aaaCCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCa                                                                            >  2:434034/1‑141 (MQ=255)

                                                                  cTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTa                                                                     >  2:367685/1‑141 (MQ=255)

                                                                     gCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACaa                                                                  >  2:198947/1‑141 (MQ=255)

                                                                        aaGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACaaaaa                                                               <  2:395933/141‑1 (MQ=255)

                                                                           gAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATgg                                                            <  1:82391/141‑1 (MQ=255)

                                                                           gAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATgg                                                            <  1:26595/141‑1 (MQ=255)

                                                                            aaTACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGc                                                           >  2:211920/1‑141 (MQ=255)

                                                                                  cATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACTCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTg                                                     <  2:237936/141‑1 (MQ=255)

                                                                                  cATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACTCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTg                                                     <  2:322371/141‑1 (MQ=255)

                                                                                  cATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACTCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTg                                                     <  2:238086/141‑1 (MQ=255)

                                                                                     ggTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTc                                                  <  2:281235/141‑1 (MQ=255)

                                                                                     ggTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTc                                                  <  2:441299/141‑1 (MQ=255)

                                                                                       ttAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCa                                                >  1:272818/1‑141 (MQ=255)

                                                                                           cacaACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCAtttt                                            >  2:5844/1‑141 (MQ=255)

                                                                                           cacaACAGTAAATGCAAAGAATGCAATTAATCCCATACCTGGTCCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCAtttt                                            >  1:234547/1‑141 (MQ=255)

                                                                                                      aTGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTg                                 <  2:33525/141‑1 (MQ=255)

                                                                                                      aTGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTg                                 <  1:420204/141‑1 (MQ=255)

                                                                                                       tGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGa                                >  2:386743/1‑141 (MQ=255)

                                                                                                       tGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGa                                >  2:386750/1‑141 (MQ=255)

                                                                                                             gAATGCATTTAATCCCATACCGTGTGCTAACGCAATTGGGTATATAGCTATTAGCCCCATGAAGTGCGATCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGcc                          <  1:42226/141‑1 (MQ=255)

                                                                                                                           ccctaacTGGTGCTAACGCAATTGTGTATTAAGCAATTAGGCCCATGAATATCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTa            <  1:434034/135‑1 (MQ=255)

                                                                                                                           ccATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTa            >  1:264794/1‑141 (MQ=255)

                                                                                                                           ccATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTa            >  1:242512/1‑141 (MQ=255)

                                                                                                                                ccTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACtt       <  1:358192/141‑1 (MQ=255)

                                                                                                                                ccTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACtt       >  1:211418/1‑141 (MQ=255)

                                                                                                                                  tGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTaa     <  1:287653/141‑1 (MQ=255)

                                                                                                                                  tGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTaa     <  1:160818/141‑1 (MQ=255)

                                                                                                                                     tGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAAc  <  1:253417/141‑1 (MQ=255)

CCCTAAACCCTGTGACGGTTAATATCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAAC  >  USA300TCH1516_ALE/2373391‑2373664

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