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 F42 I0 R1	24	30.6	687070	95.0%	652716	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,372,883	T→A	32.7%	D298V (GAT→GTT)	pbuG ←	Guanine/hypoxanthine permease PbuG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,372,883	0	T	A	32.7%	38.4 / 22.7	35	D298V (GAT→GTT)	pbuG	Guanine/hypoxanthine permease PbuG
Reads supporting (aligned to +/- strand): ref base T (15/8); new base A (2/9); total (18/17)
Fisher's exact test for biased strand distribution p-value = 2.55e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01

ATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTA  >  USA300TCH1516_ALE/2372752‑2373021

aTAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAGAACa                                                                                                                                   >  1:141712/1‑141 (MQ=255)

           caacCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAAACTGAGAACAATGCTCTACCa                                                                                                                        <  2:134208/141‑1 (MQ=255)

           caacCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTAATCATTCAATAGTAGCTAAAGAAACTGAGAACAATGCTCTACCa                                                                                                                        >  1:177254/1‑141 (MQ=255)

             acCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAGAACAATGCTCTACCAGc                                                                                                                      >  2:46160/1‑141 (MQ=255)

              ccTGTTACGATACTAGCAAATCCTGTTCTAGCACATAAAGCAACAACTGAATTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCAAAAGAACCTGAGAACAATGCTATACCatca                                                                                                                     >  2:208781/1‑138 (MQ=255)

                tGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAGAACAATGCTCTACCAGctct                                                                                                                   >  2:290771/1‑141 (MQ=255)

                        tACTAGCAAATTCTGTTCTAGCACCTTCAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAAACTGAGAACAATGCTCTACCAGCTCTTGGTAAtt                                                                                                           <  2:172914/141‑1 (MQ=255)

                                    cTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCa                                                                                               >  2:75649/1‑141 (MQ=255)

                                     tGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCat                                                                                              <  1:153522/141‑1 (MQ=255)

                                     tGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCat                                                                                              <  1:155615/141‑1 (MQ=255)

                                      gTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCata                                                                                             >  1:203225/1‑141 (MQ=255)

                                      gTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAAACTGAGAACAATGCTCTACCAGCTCTTCGTAATTTATTATCTTTCata                                                                                             >  1:10704/1‑141 (MQ=255)

                                            gCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAAACTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCt                                                                                       <  2:263801/141‑1 (MQ=255)

                                               ccTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCt                                                                                    >  1:116170/1‑141 (MQ=255)

                                                  ccAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGa                                                                                 <  1:114188/140‑1 (MQ=255)

                                                   cAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAAACTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAg                                                                                <  2:172972/141‑1 (MQ=255)

                                                      cAAAACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAg                                                                             <  2:201427/141‑1 (MQ=255)

                                                          acCTGGAGTTGATACGATATAAGAAGTTGTTGTAGTTGTTCCAAAAGCTGATCCTACAATCGTATCTAAAGTTACTGCGACAACTCCATGGCCGGCTCTTGGTAATTTAGTATCTTTCATAATTCCTGCTTGAGTAGCAAc                                                                         <  2:316904/141‑1 (MQ=255)

                                                           ccTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACa                                                                        >  1:144792/1‑141 (MQ=255)

                                                                      ttCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGt                                                             <  1:197521/141‑1 (MQ=255)

                                                                            ataAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAAACTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGc                                                       <  1:20856/141‑1 (MQ=255)

                                                                                gaagTTGTTGTAGTTGTTACAAAAACTGATCCTACAATCGTAGCTAAAGAAACTGAGAACAATGCTCTACCAGATCTTGGTAATTTATTATCTTTCATAATACCTGATTGAGTAGCAACAGCTACTAATGTACCAGCTGTa                                                   <  2:254044/141‑1 (MQ=255)

                                                                                       ttgtAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACATGCTGGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGa                                            >  2:276207/1‑141 (MQ=255)

                                                                                        tgtAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAGAACAATGCTCTACCAACTCTAAGTAATTTATTAAATGGCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGaa                                           >  2:73798/1‑141 (MQ=255)

                                                                                         gtAGTTGTTCCAAAAACTGATTCTACAATCGTAGCTAAAGAATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCATAGaaa                                          >  2:24053/1‑141 (MQ=255)

                                                                                           aGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATc                                        <  2:320471/141‑1 (MQ=255)

                                                                                                  ccAAAAACTGATCCTACAATCGTAGCTAAAGAAACTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCaataaat                                 <  1:230162/141‑1 (MQ=255)

                                                                                                         cTGATCCTACAATCGTAGCTAAAGAATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGATGTATCAAAGAAATCAATAAATAAGAACg                          >  2:286532/1‑141 (MQ=255)

                                                                                                            aTCCTACAATCCTAGCTAAAGAATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTAAGTAGCAACAGCTACTAATGTACCAGCAGTATCAAAGAAATCAATAAATAACAACGtca                       >  2:25974/1‑139 (MQ=255)

                                                                                                             tCCTACAATCGTAGCTAAAGAATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTaa                      >  2:315758/1‑141 (MQ=255)

                                                                                                                     tCGTAGCTAAAGAATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACaa              <  2:161264/141‑1 (MQ=255)

                                                                                                                       gTAGCTAAAGAAACTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAAtt            <  2:245896/141‑1 (MQ=255)

                                                                                                                               aGAATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTg    <  1:290771/141‑1 (MQ=255)

                                                                                                                                 aaTCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATGACAATTAAGAACTGTa  >  1:124575/1‑141 (MQ=255)

                                                                                                                                 aaTCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGGAGCCACAGCTACTAATGTACCAGCTGTATCAAATACATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTa  >  1:125570/1‑141 (MQ=255)

ATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTA  >  USA300TCH1516_ALE/2372752‑2373021

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A