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
A9 F59 I0 R1	41	42.9	928050	95.2%	883503	140.9

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%	107.0 / NA	35	L48L (CTA→CTT)	USA300HOU_2315	hypothetical membrane protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (14/21); total (14/21)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CAATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAAT  >  CP000730/2454491‑2454757

cAATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGGCTATAATTGTTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCAcc                                                                                                                                >  2:11949/1‑141 (MQ=255)

  aTAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACGGATCTTGCACCAt                                                                                                                              <  1:270852/141‑1 (MQ=255)

     aaaTTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTaa                                                                                                                           <  1:208646/141‑1 (MQ=255)

      aaTTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAAt                                                                                                                          >  1:355554/1‑141 (MQ=255)

        tttCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATtg                                                                                                                        >  2:103056/1‑141 (MQ=255)

            tGGTTTGCAATGGGCAATGACGCATTACGTCTTCTTTGTCATTACTATGGCGTTATCCAATATGCTCAGAGATTTCCAGTCTATAATTGGTGTGAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATtgctgc                                                                                                                    <  2:74015/141‑1 (MQ=255)

             ggTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCa                                                                                                                   <  2:203065/141‑1 (MQ=255)

             ggTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCa                                                                                                                   <  2:216244/141‑1 (MQ=255)

                     aTGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGGCTATAATTGGTGTCAAACACTTTATATTTGAGGTTACAGATCTTGCACCATTAATTGCTGCAATCAtttt                                                                                                           >  2:376855/1‑140 (MQ=255)

                       gggCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATCATAATGTTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGta                                                                                                         >  1:219279/1‑141 (MQ=255)

                       gggCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAGTCATTTGta                                                                                                         >  1:219256/1‑141 (MQ=255)

                       gggCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGta                                                                                                         <  1:395844/141‑1 (MQ=255)

                                     ttCGTCTTCTTTGGCATTACAACGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTCTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTTTACTCGTTTTCaaa                                                                                           <  2:118369/141‑1 (MQ=255)

                                           ttcttttctaTTAAAATGGCGTTATCCATTACGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATaaa                                                                                     <  2:43430/132‑1 (MQ=255)

                                                             gctttATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAAGATAAAAAGGTCCAACTTGCAGGt                                                                   <  2:330444/138‑1 (MQ=255)

                                                             gCGTTATCCATTATGCTCAGAGTTACTAAGTCGATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGt                                                                   >  1:458474/1‑141 (MQ=255)

                                                                ttATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAggatga                                                                >  2:226251/1‑137 (MQ=255)

                                                                 tATCCATTAGGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTaa                                                               <  1:179552/141‑1 (MQ=255)

                                                                   tCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTaaaa                                                             >  2:177526/1‑141 (MQ=255)

                                                                                  gaTTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTg                                              <  2:419984/141‑1 (MQ=255)

                                                                                  gaTTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTg                                              <  1:304514/141‑1 (MQ=255)

                                                                                  gaTTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTg                                              >  2:314527/1‑141 (MQ=255)

                                                                                       ccAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATAGCCCGGAAAGt                                         >  2:23295/1‑141 (MQ=255)

                                                                                           tCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAGTATAAAAAGGTCCAACTTGCAGGTTGAAAATTCGCAATCAGCCTGAAAGTAAtt                                     <  1:299593/141‑1 (MQ=255)

                                                                                                aaTTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACTATGAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACg                                <  1:85446/141‑1 (MQ=255)

                                                                                                 aTTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGt                               <  1:240474/141‑1 (MQ=255)

                                                                                                      tgtCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTAtt                          <  2:458474/141‑1 (MQ=255)

                                                                                                      tgtCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTAtt                          <  1:178863/141‑1 (MQ=255)

                                                                                                        tCAAACAGTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATGCTGGTACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGGTTAAAACTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGc                        <  1:453592/141‑1 (MQ=255)

                                                                                                             cacTTTTTATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCt                   <  1:160031/141‑1 (MQ=255)

                                                                                                                    tatTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAACGTCATTGAACGTATATTGCTAGCTTTAAttt            <  1:92732/141‑1 (MQ=255)

                                                                                                                         gAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATGAGGATGAAGGTAAGTGAACGTCTATTGCTAGCTTTAATTTTACCt       >  1:430976/1‑141 (MQ=255)

                                                                                                                         gAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCt       >  1:155041/1‑141 (MQ=255)

                                                                                                                             ttACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAACGTAATTGAACGTCTATTGCTAGCTTGAATTTTACCTTTat   >  1:373272/1‑140 (MQ=255)

                                                                                                                              tACAGTTCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAat  <  2:192546/141‑1 (MQ=255)

CAATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAAT  >  CP000730/2454491‑2454757

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A