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 F169 I0 R1	75	34.0	794130	95.7%	759982	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,279,705	G→A	100%	A943V (GCA→GTA)	ebh_3 ←	Extracellular matrix‑binding protein ebh

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,279,705	0	G	A	100.0%	115.3 / ‑6.5	41	A943V (GCA→GTA)	ebh_3	Extracellular matrix‑binding protein ebh
Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (22/18); minor base T (0/1); total (22/19)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GTTGTGCCGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGT‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGCTGT  >  USA300TCH1516_ALE/2279567‑2279841

gTTGTGCCGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGT‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACt                                                                                                                                        <  2:129141/141‑1 (MQ=255)

         ttattaGTTGATTCTACTTCTGGTTTAATAGTTACACCGTTCTCCATCGTAGGCCTGTTTGTTGATGACAATCCGTTAGGAAGGTGTAAT‑GCGTGCGTTTTATCAGTGGCATCATTAGCTTCTGTTGTTACTGTTGTTTCa                                                                                                                               >  2:329752/1‑141 (MQ=255)

             taGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGT‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTg                                                                                                                           >  2:333242/1‑141 (MQ=255)

             taGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGT‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTg                                                                                                                           >  1:82411/1‑141 (MQ=255)

             taGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGT‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTg                                                                                                                           >  1:82408/1‑141 (MQ=255)

             taGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGT‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCGGATGTTACGGTTGTTTCACCTg                                                                                                                           >  1:82412/1‑141 (MQ=255)

                ttGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGT‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTg                                                                                                                        <  2:270143/141‑1 (MQ=255)

                ttGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGT‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTg                                                                                                                        <  1:356917/141‑1 (MQ=255)

                 tGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGT‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGc                                                                                                                       >  1:138310/1‑141 (MQ=255)

                         cTTCAGGTTTACTAGTTACATCGTTATCCAATGTCGGACTGTTTGTTGATGCACCTACACTCGAATTGT‑TATTAGCTTGCGGTTTATCATTAGCATCATCAGTTCCTGATGTTACTGTTGTTTCACCTTTTGCCGGATccg                                                                                                               >  2:240921/1‑139 (MQ=255)

                            tgggTTTACTAGTTACGTTGTTTTCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGT‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACtat                                                                                                            <  2:303368/139‑1 (MQ=255)

                                            aTCGTTATCCATTGTTCGACTGTTTGTTGATGCATCTACACTATAATTGT‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCgg                                                                                            <  1:221241/141‑1 (MQ=255)

                                                  aTCCATTGTCGGCCTGTTTGTTGCTGCATCTACACTAGTATTGT‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGc                                                                                      <  1:18967/141‑1 (MQ=255)

                                                    ccATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGT‑TGTTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATGACTATTGTTTGGTGTTGTCGGAGAAGCGt                                                                                    >  2:201138/1‑141 (MQ=255)

                                                     cATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGT‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTc                                                                                   <  1:123947/141‑1 (MQ=255)

                                                            ggACTGTTTGTTGATGCATCTACACTAGAATTGT‑TATTAGCTTGCGGTTTATCAACTGCATCATCAGGTGCTGATGTTACTGTTGTTTCACATGTTGCCGCATCACTATTGTTTGGTGTTGTCGGAGACGCGTCTGCTTTg                                                                            >  2:98821/1‑141 (MQ=255)

                                                                   ttgttgATGCATCTACACTAGAATTGT‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAg                                                                     <  1:324794/141‑1 (MQ=255)

                                                                   ttgttgAGGCATCGACACTAGAATTGT‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAg                                                                     <  1:320258/141‑1 (MQ=255)

                                                                     tttgATGCATCTACATCAGAATTGC‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTTTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGTGAAGCGTCTGCTTTGCCATTAGCt                                                                   <  1:288454/140‑1 (MQ=255)

                                                                             aTCTACACTAGAATTGT‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGtctc                                                           <  2:248160/141‑1 (MQ=255)

                                                                              tCTACACTAGAATTGT‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCa                                                          >  1:216665/1‑141 (MQ=255)

                                                                               cTACACTAGAATTGT‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAg                                                         >  2:315692/1‑141 (MQ=255)

                                                                                tACACTAGAATTGT‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGa                                                        >  1:226438/1‑141 (MQ=255)

                                                                                    cTAGAATTGT‑TATTAGCTTGCGGTTTATCATTTGGAGCATCAGTTGCTGATGTTACTGGGGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACg                                                    >  2:180726/1‑141 (MQ=255)

                                                                                    cTAGAATTGT‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACg                                                    >  2:77545/1‑141 (MQ=255)

                                                                                            gT‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTg                                            >  2:215702/1‑141 (MQ=255)

                                                                                                  taGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAg                                       <  1:159444/141‑1 (MQ=255)

                                                                                                           gTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTg                              <  2:216665/141‑1 (MQ=255)

                                                                                                            tttaggaTTTGCATCATCAGTTGGTGCTGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGGTAGGTGGTCCAGTATTTGCTgg                             >  2:282554/7‑141 (MQ=255)

                                                                                                             ttATCATTTGCATTATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGgt                            <  2:138310/141‑1 (MQ=255)

                                                                                                                  aTTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGgtgtcca                       >  2:194236/1‑138 (MQ=255)

                                                                                                                   tttGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGATTTGGCATGAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCa                      >  1:388240/1‑141 (MQ=255)

                                                                                                                      gCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCAttt                   >  1:262154/1‑140 (MQ=255)

                                                                                                                           atcaGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGGTGTTGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATAGGTTGGGTTGTCCAGTATTTTTTGTTGTtgcatttgcatt              >  2:109439/1‑141 (MQ=255)

                                                                                                                            tcaGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGCAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCAttt             >  2:90751/1‑141 (MQ=255)

                                                                                                                             cacttGCTGATGTTACTGTGGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTTGCTGTCGTTTCAGATACGTTCGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTg            <  1:61758/138‑1 (MQ=255)

                                                                                                                                 tGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAAtt        >  1:52778/1‑141 (MQ=255)

                                                                                                                                   cTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTg      <  2:32418/141‑1 (MQ=255)

                                                                                                                                      aTGTTTCTTTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGCTg   <  2:180112/141‑1 (MQ=255)

                                                                                                                                      aTGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGCTg   <  2:248454/141‑1 (MQ=255)

                                                                                                                                       tGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGCTGt  <  1:333242/141‑1 (MQ=255)

GTTGTGCCGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGT‑TATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGCTGT  >  USA300TCH1516_ALE/2279567‑2279841

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