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 F104 I0 R1	54	57.6	1336546	96.4%	1288430	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,851,260	C→A	100%	A115S (GCG→TCG)	acsA_1 ←	Acetyl‑coenzyme A synthetase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,851,260	0	C	A	93.1%	99.1 / 3.4	44	A115S (GCG→TCG)	acsA_1	Acetyl‑coenzyme A synthetase
Reads supporting (aligned to +/- strand): ref base C (0/3); new base A (21/20); total (21/23)
Fisher's exact test for biased strand distribution p-value = 2.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.37e-02
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TACTCGAGGTAACAATGCCTTATTAGTAATTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGCAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGTTGCATATCTTTATAAGTATACGATT  >  USA300TCH1516_ALE/1851123‑1851388

tACCCGAGGTAACAATGCCTTATTAGTAATTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGaaaa                                                                                                                               <  1:615012/141‑1 (MQ=255)

      aGGTAACAATGCCTTATTAGTAATTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAg                                                                                                                         <  1:87059/141‑1 (MQ=255)

       ggTAACAATGCCTTATTAGTAATTAATGCTTTAGCTTCACTGTTCTCTAATCTATACGCAACTGCCTTTTCCATAAATCCTTCAAATAACGGCCCAACAATTCCACCAATTTTTTAAACACCTAACAACGAaaaaatgagt                                                                                                                        >  2:86671/1‑135 (MQ=255)

          aaCAATGCCTTATTAGTAATTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCa                                                                                                                     <  1:600291/141‑1 (MQ=255)

             aaTGCCTTATTAGTAATTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGgt                                                                                                                  <  1:304716/141‑1 (MQ=255)

              aTGCCTTATTAGTAATTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGgtg                                                                                                                 <  1:381171/141‑1 (MQ=255)

              aTGCCTTATTAGTAACTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGCAAAATATAGTTCAGgtg                                                                                                                 <  1:253036/141‑1 (MQ=255)

                gCCTTATTAGTAATTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTa                                                                                                               <  2:547503/141‑1 (MQ=255)

                  cTTATTAGTAATTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTAcg                                                                                                             <  1:244552/141‑1 (MQ=255)

                       taGTAATTACCACTTTAGCTTCACGGTTCTCTAATCTACCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACa                                                                                                        <  2:624964/141‑1 (MQ=255)

                        aGTAATTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACat                                                                                                       >  1:72392/1‑141 (MQ=255)

                        aGTAATTAACACTTTAGCTTCACTGTTCGCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTTCACCAATTTTTAAAACACCTAACAACAAAAAATATAGTTCAGGTGTACGCGACat                                                                                                       <  2:250037/141‑1 (MQ=255)

                           aaTTTATACTTTTTCTTCACTCTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCACCACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATTGTTCATGAGTACGCCAAataaa                                                                                                    >  2:56105/1‑141 (MQ=255)

                           aaTTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTACAGCACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACataaa                                                                                                    >  2:269363/1‑141 (MQ=255)

                              tAACACTTTAGCTTCACTTTTCTCTAATCTATCCGCAACAGCCTTTTCCATAAATGCTTCAAATAACGTCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGCAAAATATAGTTCAGGTGTACGCGACatatatat                                                                                                 <  2:461893/141‑1 (MQ=255)

                              tAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACataaatat                                                                                                 <  1:161098/141‑1 (MQ=255)

                                       aGCTTCACTGTTCTCTACTCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATActct                                                                                        <  1:262797/141‑1 (MQ=255)

                                        gCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTGACAGAGTTTATTCAACAGAGGGGCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTg                                                                                       >  1:319514/1‑141 (MQ=255)

                                                   ctctAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACCTAACTATAAAAACTCTGTCACCTTTGTc                                                                            >  2:328929/1‑141 (MQ=255)

                                                    tctAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATCACAGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCa                                                                           >  1:456740/1‑141 (MQ=255)

                                                     ctAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCaa                                                                          >  1:386116/1‑141 (MQ=255)

                                                     ctAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAAATGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCaa                                                                          >  2:477315/1‑141 (MQ=255)

                                                           tATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCAGCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGTTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTg                                                                    <  2:366602/141‑1 (MQ=255)

                                                           tATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTg                                                                    >  2:38214/1‑141 (MQ=255)

                                                            aTCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGc                                                                   <  2:623333/141‑1 (MQ=255)

                                                             tCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCCACCATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCa                                                                  >  2:436139/1‑141 (MQ=255)

                                                               cGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGGCACCTTTGTCAACTTCTGCATg                                                                >  2:219203/1‑141 (MQ=255)

                                                                 cAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACACTTGCACCAATTTTTAAAACACCTAACCACGAAAAATATAGTTCAGGTGTACGCGACATAAATGTAACTACTCTGTCACCTGTTTCCACTGCCGCATGtc                                                              >  2:77260/1‑140 (MQ=255)

                                                                 cAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGtt                                                              >  2:495671/1‑141 (MQ=255)

                                                                       ccTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCATTACCACCTTCTGCACGTACAGACa                                                        >  2:291777/1‑141 (MQ=255)

                                                                             ccATAAATGCTTCAAATAACGGCCCAGCAATTGCACCAATTTTTAAAACACCTAACAACGCAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACAt                                                  <  2:460563/141‑1 (MQ=255)

                                                                             ccATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACAt                                                  >  2:379487/1‑141 (MQ=255)

                                                                              cATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACAtt                                                 >  1:336404/1‑141 (MQ=255)

                                                                                  aaTGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACGCCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCgct                                             >  2:470466/1‑141 (MQ=255)

                                                                                       ttCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAAAACTCTCTCACCTTTGTCGACTTCTGCATGTTCAGACAAAACATTCACTGCttt                                        >  2:505478/1‑141 (MQ=255)

                                                                                       ttCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGAAATAAATATAAAAACTATGTTACCTTTGTCAATTTCTGCAGGTACAGACAAAACATTCGCTGCttt                                        >  2:433771/1‑141 (MQ=255)

                                                                                           aaTAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATCAATACTCTGTCACCTTTGTCACCTTCTGCATGTTCAGACAAACAATTCGCTGCTttgtta                                    >  2:508575/1‑141 (MQ=255)

                                                                                                    ccAACAATTGCACCAAGTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGt                           <  2:575708/141‑1 (MQ=255)

                                                                                                        caaTTGCACCATTTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGTTGCa                       <  2:524575/141‑1 (MQ=255)

                                                                                                        caaTTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGTTGCa                       <  2:454874/141‑1 (MQ=255)

                                                                                                        caaTTGCACCAATTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGTTGCa                       <  2:118601/141‑1 (MQ=255)

                                                                                                                  aaTTTTTAAAACACCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGTTGCATATCTTtata             <  1:328929/141‑1 (MQ=255)

                                                                                                                       ttAAAACTCCTAACAACGAAAAATATAGTTCAGGTGTACGCAACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGTTGCATATCTTTATAAGtat        <  2:258540/141‑1 (MQ=255)

                                                                                                                       ttAAAACACCTGACAACGAAAAATATAGTTCAGGTGTACGCAACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGTTGCATATCTTTATAAGtat        <  2:258611/141‑1 (MQ=255)

                                                                                                                             cacCTAACAACGAAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGTTGCATATCTTTATAAGTAGACGAtt  <  2:407589/141‑1 (MQ=255)

TACTCGAGGTAACAATGCCTTATTAGTAATTAACACTTTAGCTTCACTGTTCTCTAATCTATCCGCAACTGCCTTTTCCATAAATGCTTCAAATAACGGCCCAACAATTGCACCAATTTTTAAAACACCTAACAACGCAAAATATAGTTCAGGTGTACGCGACATAAATATAAATACTCTGTCACCTTTGTCAACTTCTGCATGTTCAGACAAAACATTCGCTGCTTTATTAGATAACCGTTGCATATCTTTATAAGTATACGATT  >  USA300TCH1516_ALE/1851123‑1851388

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