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
A7 F123 I0 R1	30	27.0	575273	98.7%	567794	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,470,111	G→A	50.0%	S575L (TCA→TTA)	emrB ←	Multidrug export protein EmrB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,470,111	0	G	A	50.0%	‑4.0 / 34.5	26	S575L (TCA→TTA)	emrB	Multidrug export protein EmrB
Reads supporting (aligned to +/- strand): ref base G (6/7); new base A (3/10); total (9/17)
Fisher's exact test for biased strand distribution p-value = 4.11e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAAAATTAAGGCGATGATGCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTACCTATAGAGCCTGCTAAT  >  USA300TCH1516_ALE/2469984‑2470245

tAAAATTAAGGCGATGATGCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATg                                                                                                                           <  1:554914/141‑1 (MQ=255)

      tAAGTCGATGATGCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATg                                                                                                                     <  1:29924/141‑1 (MQ=255)

         ggCGATGATGCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATc                                                                                                                  >  1:67189/1‑141 (MQ=255)

                    tAAATATCGTTGTAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAATTTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATAGTGATGCTAATTCATGCATATGATCTTGTACAACAg                                                                                                       <  1:397480/141‑1 (MQ=255)

                     aaaTATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAgg                                                                                                      <  1:238780/141‑1 (MQ=255)

                                           tcatcatTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTcc                                                                                <  1:519237/140‑1 (MQ=255)

                                           gCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGACTTCTTGTCCGCCATATTGTAATGCTAATTCATGTATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTcc                                                                                <  1:387111/141‑1 (MQ=255)

                                                  tAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAg                                                                         >  1:483282/1‑141 (MQ=255)

                                                    aTACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCt                                                                       <  1:509528/141‑1 (MQ=255)

                                                     tACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAATACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTg                                                                      <  1:27052/141‑1 (MQ=255)

                                                                 ttGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTtgtg                                                          >  1:209224/1‑141 (MQ=255)

                                                                        tttatttaCAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAATAGCTGATAAGTGTTGTGTTGTTtg                                                   >  1:355532/1‑141 (MQ=255)

                                                                          tatttaCAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTtgtg                                                 <  1:53616/141‑1 (MQ=255)

                                                                                 aaaTTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCAt                                          >  1:499249/1‑141 (MQ=255)

                                                                                          taACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCCTTACAGTagc                                 >  1:222093/1‑139 (MQ=255)

                                                                                               cTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGa                            >  1:176788/1‑141 (MQ=255)

                                                                                               cTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGa                            <  1:161455/141‑1 (MQ=255)

                                                                                               cTTTCATTGCGCCTTCTTGGCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGa                            <  1:193472/141‑1 (MQ=255)

                                                                                                tttCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAACGCGGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGAt                           <  1:325410/141‑1 (MQ=255)

                                                                                                    aTTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGGTAAGTGTTGTGTAGTTTGTGTTGTCATTAGAGTAACTAAGATTGCt                       >  1:485118/1‑141 (MQ=255)

                                                                                                      tGCCCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTGCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGt                     <  1:429523/141‑1 (MQ=255)

                                                                                                       gcgcCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTa                    >  1:570942/1‑141 (MQ=255)

                                                                                                         gcCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTAcc                  <  1:370380/141‑1 (MQ=255)

                                                                                                            ttcttGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTACCtat               <  1:67773/141‑1 (MQ=255)

                                                                                                                         tatTGTAATGCTAATTGCTGCATTTGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTACCTATAGAGCCTGCTAAt  <  1:416357/141‑1 (MQ=255)

                                                                                                                         tatTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTTTTCTCATTACAGTAACTAAGATTGCTGTACCTATAGAGCCTGCTAAt  <  1:416515/141‑1 (MQ=255)

TAAAATTAAGGCGATGATGCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTACCTATAGAGCCTGCTAAT  >  USA300TCH1516_ALE/2469984‑2470245

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `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