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
A5 F1 I1 R1	81	47.9	2225048	94.8%	2109345	113.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,722,854	T→C	L245P (CTC→CCC)	ydhK →	putative efflux protein (PET) component of YdhJK efflux pump

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,722,854	0	T	C	100.0%	117.9 / NA	33	L245P (CTC→CCC)	ydhK	putative efflux protein (PET) component of YdhJK efflux pump
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (13/20); total (13/20)

GAAACAACCGATGCCATTCGTGCAGCACATGAAGGGGTGATTGGGCAGATACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCGACGTATGTTGCTCAACTGGCCCTCACCGCCAGGTGCCACACGAGAAATTCTCGAACAGTTGCTGACGGCGCTCGCCAGTTCGCAAACA  >  NC_000913/1722721‑1722984

gAAACAACCGATGCCATTCGTGCAGCACATGAAGGGGTGATTGGGCAGATACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCccacc                                                                                                                               <  1:634843/139‑1 (MQ=255)

  aacaacCGATGCCATTCGTGCAGCACATGAAGGGGTGATTGGGCAGATACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCCCACCAg                                                                                                                             <  1:826816/139‑1 (MQ=255)

      acCGATGCCATTCGTGCAGCACATGAAGGGGTGATTGGGCAGATACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCCCACCAGCAAt                                                                                                                         <  1:511793/139‑1 (MQ=255)

       ccGATGCCATTCGTGCAGCACATGAAGGGGTGATTGGGCAGATACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCCCACCAg                                                                                                                             <  1:763313/134‑1 (MQ=255)

       ccGATGCCATTCGTGCAGCACATGAAGGGGTGATTGGGCAGATACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCCCACCAg                                                                                                                             >  2:763313/1‑134 (MQ=255)

           tGCCATTCGTGCAGCACATGAAGGGGTGATTGGGCAGATACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCCCACCAGCAATTACGt                                                                                                                    >  1:862718/1‑139 (MQ=255)

            gCCATTCGTGCAGCACATGAAGGGGTGATTGGGCAGATACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCccacc                                                                                                                               <  2:713547/127‑1 (MQ=255)

            gCCATTCGTGCAGCACATGAAGGGGTGATTGGGCAGATACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCccacc                                                                                                                               >  1:713547/1‑127 (MQ=255)

                        gcaCATGAAGGGTTGATTGGGCAGATACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCCCTGCCCCACCAGCAATTACGTATGACCAGTCTCa                                                                                                       >  1:542056/1‑139 (MQ=255)

                                   ggTGATTGGGCAGATACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCCCACCAGCAATTACGt                                                                                                                    >  1:508420/1‑115 (MQ=255)

                                   ggTGATTGGGCAGATACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCCCACCAGCAATTACGt                                                                                                                    <  2:508420/115‑1 (MQ=255)

                                   ggTGATTGGGCAGATACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTg                                                                                            >  2:123871/1‑139 (MQ=255)

                                   ggTGATTGGGCAGATACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTg                                                                                            >  2:1029906/1‑139 (MQ=255)

                                     tGATTGGGCAGATACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCg                                                                                          <  1:606068/139‑1 (MQ=255)

                                       aTTGGGCAGATACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCGAc                                                                                        <  2:284200/139‑1 (MQ=255)

                                                      aCCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCccacca                                                                                                                              >  1:510848/1‑86 (MQ=255)

                                                      aCCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCccacca                                                                                                                              <  2:510848/86‑1 (MQ=255)

                                                      aCCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCGACGTATGTTGCTCAACt                                                                         >  1:725402/1‑139 (MQ=255)

                                                         aTGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCGACGTATGTTGCTCAACTGGc                                                                      <  2:587097/139‑1 (MQ=255)

                                                            aaTTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCGACGTATGTTGCTCAACTGGCCCt                                                                   <  1:1029906/139‑1 (MQ=255)

                                                                tgctgcGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGTCTg                                                                                            >  2:41583/1‑110 (MQ=255)

                                                                tgctgcGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCGACGTATGTTGCTCAACTGGCCCTCAcc                                                               >  2:76875/1‑139 (MQ=255)

                                                                tgctgcGTATCCAGGCGTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGTCTg                                                                                            <  1:41583/110‑1 (MQ=255)

                                                                  ctgcGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCATCAAAACGCGCGCCTTAATGCGCTGCCCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCGACGTATGTTGCTCAACTGGCCCTCACCGc                                                             <  1:666348/139‑1 (MQ=255)

                                                                             ggCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCCCACCAGCaa                                                                                                                          >  1:529023/1‑67 (MQ=255)

                                                                             ggCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCCCACCAGCaa                                                                                                                          <  2:529023/67‑1 (MQ=255)

                                                                                          cACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCCCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCGACGTATGTTGCTCAACTGGCCCTCACCGCCAGGTGCCACACGAGAAATTCTCg                                     <  2:1005678/139‑1 (MQ=255)

                                                                                                      cGCCAGCAAAACGCGCGCCTTAATGCGCTGCCCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCGACGTATGTTGCTCAACTGGc                                                                      <  2:165272/94‑1 (MQ=255)

                                                                                                      cGCCAGCAAAACGCGCGCCTTAATGCGCTGCCCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCGACGTATGTTGCTCAACTGGc                                                                      >  1:165272/1‑94 (MQ=255)

                                                                                                                aCGCGCGCCTTAATGCGCTGCCCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCGACGTATGTTGCTCAACTGGCCCTCACCGCCAGGTGCCACACGAGAAATTCTCGAACAGTTGCTGACGGCGCTCGc               <  2:928918/139‑1 (MQ=255)

                                                                                                                           aaTGCGCTGCCCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCGACGTATGTTGCTCAACTGGCCCTCACCGCCAGGTGCCACACGAGAAATTCTCGAACAGTTGCTGACGGCGCTCGCCAGTTCGCaaa    <  1:72037/139‑1 (MQ=255)

                                                                                                                             tGCGCTGCCCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCGACGTATGTTGCTCAACTGGCCCTCACCGCCAGGTGCCACACGAGAAATTCTCGAACAGTTGCTGACGGCGCTCGCCAGTTCGCAAACa  <  1:260916/139‑1 (MQ=255)

                                                                                                                             tGCGCTGCCCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCGACGTATGTTGCTCAACTGGCCCTCACCGCCAGGTGCCACACGAGAAATTCTCGAACAGTTGCTGACGGCGCTCGCCAGTTCGCAAACa  <  1:123871/139‑1 (MQ=255)

GAAACAACCGATGCCATTCGTGCAGCACATGAAGGGGTGATTGGGCAGATACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCGACGTATGTTGCTCAACTGGCCCTCACCGCCAGGTGCCACACGAGAAATTCTCGAACAGTTGCTGACGGCGCTCGCCAGTTCGCAAACA  >  NC_000913/1722721‑1722984

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A