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	2,373,714	C→T	33.3%	G21D (GGT→GAT)	pbuG ←	Guanine/hypoxanthine permease PbuG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,373,714	0	C	T	33.3%	53.9 / 35.6	45	G21D (GGT→GAT)	pbuG	Guanine/hypoxanthine permease PbuG
Reads supporting (aligned to +/- strand): ref base C (11/19); new base T (9/6); total (20/25)
Fisher's exact test for biased strand distribution p-value = 2.05e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.15e-01

CAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTAATAGTTTAATATCATTCTTAATAAAAAACAATACCAAAAGCGAACTTT  >  USA300TCH1516_ALE/2373574‑2373854

cAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATAc                                                                                                                                              >  2:322967/1‑141 (MQ=255)

cAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATAc                                                                                                                                              >  2:66488/1‑141 (MQ=255)

cAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATAc                                                                                                                                              >  1:27311/1‑141 (MQ=255)

        gctAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATATCGCCTAAg                                                                                                                                      >  2:265458/1‑141 (MQ=255)

         ctAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAGCTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGa                                                                                                                                     <  2:444018/141‑1 (MQ=255)

             tGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTtc                                                                                                                                 <  1:282763/141‑1 (MQ=255)

             tGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTtc                                                                                                                                 <  1:93151/141‑1 (MQ=255)

             tGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTtc                                                                                                                                 <  1:184214/141‑1 (MQ=255)

                    gCTACAAAGATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAGACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATATCGCCTAAGATTTCTCTTTTa                                                                                                                          <  1:69030/141‑1 (MQ=255)

                      tACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTaaa                                                                                                                        <  1:82251/141‑1 (MQ=255)

                      tACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTaaa                                                                                                                        <  1:334751/141‑1 (MQ=255)

                               ggCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATATCGCCTAAGATTTCTCTTTTAAAGTTTGTTcc                                                                                                               >  2:247453/1‑141 (MQ=255)

                               ggCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATATCGCCTAAGATTTCTCTTTTAAAGTTTGTTcc                                                                                                               >  2:29506/1‑141 (MQ=255)

                               ggCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGCTAACTGCTAACATATAGGCCATAGA‑TAAGAAAGTTGTGATATCGCCTAAGATTTCTCTTTTAAAGTTTGTTcc                                                                                                               >  1:240634/1‑141 (MQ=255)

                                 cACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATATCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCat                                                                                                             >  2:307522/1‑141 (MQ=255)

                                  aCCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATATCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCata                                                                                                            <  1:198947/141‑1 (MQ=255)

                                       ggTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTAt                                                                                                       <  1:211920/141‑1 (MQ=255)

                                                 cATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATATCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGaa                                                                                             >  1:65808/1‑141 (MQ=255)

                                                   tatCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAAt                                                                                           <  2:27311/141‑1 (MQ=255)

                                                   tatCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAAt                                                                                           <  1:322967/141‑1 (MQ=255)

                                                   tatCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAAt                                                                                           <  1:66488/141‑1 (MQ=255)

                                                              aCGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACg                                                                                <  2:14959/141‑1 (MQ=255)

                                                              aCGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACg                                                                                <  2:392035/141‑1 (MQ=255)

                                                                gCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGATTAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGa                                                                               >  1:253715/1‑141 (MQ=255)

                                                                gCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATATCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGaa                                                                              >  1:392378/1‑141 (MQ=255)

                                                                  cTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATATCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATg                                                                            <  2:65808/141‑1 (MQ=255)

                                                                  cTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATg                                                                            >  2:222637/1‑141 (MQ=255)

                                                                            tGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATATCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCtt                                                                  <  1:386750/141‑1 (MQ=255)

                                                                            tGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATATCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCtt                                                                  <  1:386743/141‑1 (MQ=255)

                                                                                aaaCTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCtttttt                                                              <  1:357919/141‑1 (MQ=255)

                                                                                   cTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAGCTGGAAATAGTTTTTCACGAATGGATGCTCCTTCTTTTaa                                                           <  2:264794/141‑1 (MQ=255)

                                                                                   cTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTaa                                                           <  2:242512/141‑1 (MQ=255)

                                                                                      aaaaCTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAAt                                                        >  2:213979/1‑141 (MQ=255)

                                                                                      aaaaCTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAAt                                                        >  2:459581/1‑141 (MQ=255)

                                                                                          cTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTATAATACCt                                                    <  1:365261/141‑1 (MQ=255)

                                                                                          cTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCt                                                    <  1:352213/141‑1 (MQ=255)

                                                                                             gCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATATCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTTAAATACCTTaa                                                 >  2:411344/1‑141 (MQ=255)

                                                                                             gCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATATCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTTAAATACCTTaa                                                 >  2:394071/1‑141 (MQ=255)

                                                                                                         cTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTAATAGTTTAATATc                                     <  2:211418/141‑1 (MQ=255)

                                                                                                                ataGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTAATAGTTTAATATCATTCTta                              >  2:251154/1‑141 (MQ=255)

                                                                                                                   ggCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGATCCTTTTTTTAAAATAGCTTAATATTTTAATATCATTCTtaata                           >  1:133644/1‑141 (MQ=255)

                                                                                                                    gCCATAGA‑TAAGAAAGTTGTGATGCCGCCTGAGATTTCTCTTTTAAAGTTTGTTGCATATTTATCGAACTAGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTAGTAGTTTAATATTATTCTtaataa                          <  2:303096/141‑1 (MQ=255)

                                                                                                                    gCCATAGA‑TAAGAAAGTTGTGATATCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTAATAGTTTAATATCATTCTtaataa                          <  1:5844/141‑1 (MQ=255)

                                                                                                                           a‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTAATAGTTTAATATCATTCTTAATAAAAAACaa                   >  2:94860/1‑141 (MQ=255)

                                                                                                                           a‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTAATAGTTTAATATCATTCTTAATAAAAAACaa                   >  2:165490/1‑141 (MQ=255)

                                                                                                                                   aGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTAATAGTTTAATATCATTCTTAATATAATACAATatccaa            >  2:122367/1‑136 (MQ=255)

                                                                                                                                   aGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTAATAGTTTAATATCATTCTTAATAAAAAACAATACCaaa            >  2:145093/1‑141 (MQ=255)

                                                                                                                                         gATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTAATAGTTTAATATCATTCTTAATAAAAAACAATACCAAAAGCGaa      >  2:35670/1‑141 (MQ=255)

                                                                                                                                             ccGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCTAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTAATAGTTTAATATCATTCTTAATAAAAAACAATACCAAAAGCGAACtct  >  1:181645/1‑139 (MQ=255)

CAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTAATAGTTTAATATCATTCTTAATAAAAAACAATACCAAAAGCGAACTTT  >  USA300TCH1516_ALE/2373574‑2373854

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

GATK/CNVnator alignment

N/A