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
A17 F13 I0 R1	90	33.2	766976	92.9%	712520	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	479,553	G→A	100%	A194T (GCA→ACA)	USA300HOU_0458 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	479,553	0	G	A	100.0%	103.0 / NA	34	A194T (GCA→ACA)	USA300HOU_0458	hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (14/20); total (14/20)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATGCATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCA‑TTTTTCAATAGATCAGGAAGACTAC  >  CP000730/479422‑479687

cAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGc                                                                                                                                <  1:278702/141‑1 (MQ=255)

    aataGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCAttt                                                                                                                            >  2:205998/1‑141 (MQ=255)

     ataGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTa                                                                                                                           >  2:102365/1‑141 (MQ=255)

     ataGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATAGTTGCATTTa                                                                                                                           >  2:188608/1‑141 (MQ=255)

      taGATGAACAAGGTGAGCCACTTAGCAAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAg                                                                                                                          >  2:238125/1‑141 (MQ=255)

            aaCAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGAAAGAGACAAGTTTTTACCATACATGGTTGCATTTAggcgaac                                                                                                                    >  1:104418/1‑135 (MQ=255)

                aGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGa                                                                                                                <  1:174225/141‑1 (MQ=255)

                aGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGa                                                                                                                <  1:194436/141‑1 (MQ=255)

                  gTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGAcc                                                                                                              <  1:40782/141‑1 (MQ=255)

                       ccACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGt                                                                                                         <  1:222115/141‑1 (MQ=255)

                                           tCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATATATGGTTGCATTTAGCGCAACATGACTTTTGTTTTACTAAAGCACAGCGCCa                                                                                     <  2:271448/141‑1 (MQ=255)

                                             gTCATAGGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTCACTAAAGCACAGCGCCAAg                                                                                   <  1:203318/141‑1 (MQ=255)

                                             gTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAg                                                                                   <  1:184601/141‑1 (MQ=255)

                                                   agATCAAATCGACCAAACCTTATATCGATCAATTTCTATCGAGTTCAACAATGCCGAAGCGTCCGCAAACTTTTTACCCAACATCGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTa                                                                             <  2:366662/140‑1 (MQ=255)

                                                        aaaTGGACGAAACTTTCTATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGc                                                                        <  1:115871/141‑1 (MQ=255)

                                                           tGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTa                                                                     >  2:217107/1‑141 (MQ=255)

                                                               cGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACAGGACCATAGTTTTACTACAGAACAGCGCCAAGTCAGAAAAGGCGTCCCCa                                                                 >  1:50577/1‑141 (MQ=255)

                                                                     tttATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACTGCGCCAAGTGATTAAAGGCTTACCCAATGATc                                                           <  1:273999/141‑1 (MQ=255)

                                                                         tatCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGa                                                       >  1:291031/1‑141 (MQ=255)

                                                                                     tatATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATaga                                           <  2:188360/139‑1 (MQ=255)

                                                                                       tATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGt                                         >  2:141378/1‑141 (MQ=255)

                                                                                                 gACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAAc                               <  2:181350/141‑1 (MQ=255)

                                                                                                      tGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCA‑tt                         <  1:217030/141‑1 (MQ=255)

                                                                                                       gCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGATTTACGAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAACGATCCTGAAATGACGATAGAGTCAGTATTAACTCA‑ttt                        >  2:215554/1‑141 (MQ=255)

                                                                                                        ccGAAGCGTGAGCAAAGTTTTTACCGTACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTGACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCA‑tttt                       <  2:244463/141‑1 (MQ=255)

                                                                                                        ccGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCA‑tttt                       <  1:195139/141‑1 (MQ=255)

                                                                                                        ccGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCA‑tttt                       <  2:189739/141‑1 (MQ=255)

                                                                                                         cGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACACAATGATCCTGAAGTGACGATAGGGTCAGTATTAACTCC‑ttttt                      >  1:174975/1‑141 (MQ=255)

                                                                                                          gAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGTGTCAGTCTTAACTCA‑TTTTTc                     >  1:18684/1‑141 (MQ=255)

                                                                                                                tGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCCGGATACACTCA‑TTTTTCAATAGa               >  2:1689/1‑141 (MQ=255)

                                                                                                                      aaGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGACATGACGATAGAGTCAGTATTAACTCATTTTTTCAATAGATCAgg          <  1:216377/141‑1 (MQ=255)

                                                                                                                          ttttACCACACATGGTTGCATTTAGCGCAACATGACCATAGTTTTAATAAAGCGCAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCA‑TTTTTCAATAGATCAGGAAGAc     <  1:165963/141‑1 (MQ=255)

                                                                                                                            ttACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCA‑TTTTTCAATAGATCAGGAAGACTa   >  2:189657/1‑141 (MQ=255)

                                                                                                                             tACCATACCTGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCA‑TTTTTCAATAGATCAGGAAGACTAc  <  1:313173/141‑1 (MQ=255)

CAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATGCATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCA‑TTTTTCAATAGATCAGGAAGACTAC  >  CP000730/479422‑479687

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