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	46	52.8	1143652	95.1%	1087613	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,454,626	A→T	100%	L48L (CTA→CTT)	USA300HOU_2315 →	hypothetical membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,454,626	0	A	T	100.0%	101.9 / ‑6.5	34	L48L (CTA→CTT)	USA300HOU_2315	hypothetical membrane protein
Reads supporting (aligned to +/- strand): ref base A (0/0); major base T (24/9); minor base G (1/0); total (25/9)
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.

ACAATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAATTATT  >  CP000730/2454490‑2454761

aCAATAAAATTTGTGGGTTTCAATGGGCAATGACGATTTGCGTATTCTTTGTTAATACACTGGCGGTATCCATTATGCTCAGAGATTTCCGGTCTATAATTGCCGTCCACCACTTTTTATTTTAAGTTACAGATTTTGCAc                                                                                                                                     >  1:75395/1‑141 (MQ=255)

aCAATAAAATTTCTGGTTTTCAATGAGCAATGACGATATTCGGCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGCAGTTAAAGATCTGGCAc                                                                                                                                     >  2:242338/1‑141 (MQ=255)

    tAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCAtt                                                                                                                                 >  2:194529/1‑141 (MQ=255)

           tCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATtgct                                                                                                                          <  1:194529/141‑1 (MQ=255)

              ggTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCa                                                                                                                       <  1:79059/141‑1 (MQ=255)

                      aTGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTg                                                                                                               >  2:393866/1‑141 (MQ=255)

                        gggCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGta                                                                                                             >  1:492020/1‑141 (MQ=255)

                         ggCAATGACGATTTTCGTCTTCTTTGCACTTTTAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGtac                                                                                                            >  2:97225/1‑140 (MQ=255)

                               gACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTCCCCGCCCATAATTGGTGCCAAACACTTTATATTCGAAGTTACCGCTCTTGCCCCCTTCCTCGCCGCAACCCTTTGtctccccgc                                                                                                      >  2:388653/1‑133 (MQ=255)

                                aCGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGTTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGtt                                                                                                     >  1:78365/1‑141 (MQ=255)

                                aCGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGtt                                                                                                     >  1:515322/1‑141 (MQ=255)

                                           cttcttTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATaa                                                                                          >  1:457873/1‑141 (MQ=255)

                                                     aTTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTCTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGAACTCATTTGTATACTCGTTTTCAAACATAAAAAGGTCCac                                                                                >  2:106187/1‑140 (MQ=255)

                                                       tACAATGGCGTAATCCATTATGCTCAGAGATATCCAGTCTATAATTGGTGTCAAACACTTTATAGTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCTAATATAAAAAGGTCCAACt                                                                              <  1:303375/141‑1 (MQ=255)

                                                        aCAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACtt                                                                             >  1:398706/1‑141 (MQ=255)

                                                        aCAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACACGTTTTCAATTATAACAGGGTGCAACtt                                                                             >  1:165778/1‑141 (MQ=255)

                                                          aaTGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGGCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGc                                                                           >  1:302215/1‑141 (MQ=255)

                                                                     ccATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAAt                                                                >  1:552523/1‑141 (MQ=255)

                                                                       aTTATGCTCAGAGATTTCCAATCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATtc                                                              >  1:348256/1‑141 (MQ=255)

                                                                             cTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAAta                                                        >  1:248003/1‑140 (MQ=255)

                                                                                   gaTTTCCAGTCCATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTg                                                  <  1:147358/141‑1 (MQ=255)

                                                                                                taATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAAc                                     >  1:496243/1‑141 (MQ=255)

                                                                                                       tgtCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAGGTAATTGAACGTCTAtt                              >  1:138638/1‑141 (MQ=255)

                                                                                                               acTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCtt                      <  1:393866/141‑1 (MQ=255)

                                                                                                                 tttATATTTGAAGTTACAGATCTTGCACCACTAAATGCTCCAATCATTAGTATACTAGTCCTCCCCTATACAACGGCCCAAATTACAGGCTGATAATGCTCAATCATCCAGAAAGTTATCGAACGCCTATTGTTAGCTTTa                    >  2:331667/1‑141 (MQ=255)

                                                                                                                 tttATATTTGAAGCTACAGAGCTTGCACCATTAATTGCTACAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTTCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTa                    <  1:191496/141‑1 (MQ=255)

                                                                                                                    atatTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAAtt                 >  1:14143/1‑141 (MQ=255)

                                                                                                                     tatTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAAttt                <  2:78365/141‑1 (MQ=255)

                                                                                                                          gAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCt           >  2:257807/1‑141 (MQ=255)

                                                                                                                             gTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTa        >  1:35137/1‑141 (MQ=255)

                                                                                                                              ttACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTaa       <  1:258009/141‑1 (MQ=255)

                                                                                                                              gtACAGATCTTGCACCATTAATTTCTGCAATCATTTGTATTCTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTaa       <  2:140501/140‑1 (MQ=255)

                                                                                                                                 cAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAatta    >  1:416107/1‑141 (MQ=255)

                                                                                                                                   gATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAattatt  >  1:228097/1‑141 (MQ=255)

ACAATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAATTATT  >  CP000730/2454490‑2454761

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