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
A3 F1 I1 R1	781	46.9	2231650	93.5%	2086592	109.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,796,916	T→C	Y38C (TAT→TGT)	yqaE ←	cyaR sRNA‑regulated protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,796,916	0	T	C	100.0%	162.9 / NA	45	Y38C (TAT→TGT)	yqaE	cyaR sRNA‑regulated protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (23/22); total (23/22)

ACCCATAGCTACCTCATTCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATATACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAACCCATATGTACTCCC  >  NC_000913/2796781‑2797038

aCCCATAGCTACCTCATTCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACAcc                                                                                                                         >  2:58843/1‑139 (MQ=255)

   cATAGCTACCTCATTCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCaa                                                                                                                      <  1:209017/139‑1 (MQ=255)

            cTCATTCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCa                                                                                                             >  2:607305/1‑139 (MQ=255)

              cATTCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAAc                                                                                                           <  1:1017362/139‑1 (MQ=255)

                ttCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGc                                                                                                                    >  2:927677/1‑128 (MQ=255)

                ttCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGc                                                                                                                    <  1:927677/128‑1 (MQ=255)

                ttCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAg                                                                                                         >  2:53860/1‑139 (MQ=255)

                ttCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAAGCAAACCGGGGATACACCCAAGCAGTGTCAACAg                                                                                                         >  1:1107035/1‑139 (MQ=255)

                                 tCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACg                                                                                        >  2:179346/1‑139 (MQ=255)

                                        gtgtAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAAcc                                                                                 <  1:179346/139‑1 (MQ=255)

                                                 agGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAat                                                                                                      <  1:135683/109‑1 (MQ=255)

                                                 agGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAat                                                                                                      >  2:135683/1‑109 (MQ=255)

                                                   gAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTAc                                                                      >  1:22029/1‑139 (MQ=255)

                                                   gAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTAc                                                                      >  2:390134/1‑139 (MQ=255)

                                                     aCGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAgtgt                                                                                                               >  1:655194/1‑96 (MQ=255)

                                                     aCGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCAGGGATACACCCAAGCAgtgt                                                                                                               <  2:655194/96‑1 (MQ=255)

                                                      cgcgGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAg                                                                                                         >  1:675796/1‑101 (MQ=255)

                                                      cgcgGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAg                                                                                                         <  2:675796/101‑1 (MQ=255)

                                                      cgcgGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAAcc                                                                                 <  2:908591/125‑1 (MQ=255)

                                                      cgcgGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAAcc                                                                                 >  1:908591/1‑125 (MQ=255)

                                                                          gggATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTa                                                                       >  2:784346/1‑115 (MQ=255)

                                                                          gggATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTa                                                                       <  1:784346/115‑1 (MQ=255)

                                                                          ggatggAGCACAGGTTTAATCCGGGGTTTGCCCCCAGAACGCGTGAATCAAA‑CGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCTTTTACCGAGCAGCACGCCGAGCGGCGGCa                                              <  2:677126/134‑1 (MQ=255)

                                                                                aGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAatg                                         >  2:915369/1‑139 (MQ=255)

                                                                                 gCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAatga                                        <  1:607305/139‑1 (MQ=255)

                                                                                      ggTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAg                                                                                                         >  1:487413/1‑69 (MQ=255)

                                                                                      ggTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAg                                                                                                         <  2:487413/69‑1 (MQ=255)

                                                                                       gTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAAc                                                                                                           <  2:1085194/66‑1 (MQ=255)

                                                                                       gTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAAc                                                                                                           >  1:506846/1‑66 (MQ=255)

                                                                                       gTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAAc                                                                                                           >  1:1085194/1‑66 (MQ=255)

                                                                                       gTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAAc                                                                                                           <  2:506846/66‑1 (MQ=255)

                                                                                             tCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGa                            >  2:801052/1‑139 (MQ=255)

                                                                                                 gggTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATtct                        >  2:541265/1‑139 (MQ=255)

                                                                                                    tttGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCa                     <  2:22029/139‑1 (MQ=255)

                                                                                                       gCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGaa                  <  1:541265/139‑1 (MQ=255)

                                                                                                          cccAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAAcc               <  1:801052/139‑1 (MQ=255)

                                                                                                            cAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCAAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAACCCa             >  1:345441/1‑139 (MQ=255)

                                                                                                             aGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAg                    >  1:892805/1‑131 (MQ=255)

                                                                                                             aGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAg                    <  2:892805/131‑1 (MQ=255)

                                                                                                               aaCGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAACCCatat          >  1:1002534/1‑139 (MQ=255)

                                                                                                                  gcgTGAATCAAACCGGGGATACACCCAAGCAGTGTCaa                                                                                                            <  2:573319/38‑1 (MQ=255)

                                                                                                                  gcgTGAATCAAACCGGGGATACACCCAAGCAGTGTCaa                                                                                                            >  1:573319/1‑38 (MQ=255)

                                                                                                                  gcgTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAACCCATATGTa       <  2:280529/139‑1 (MQ=255)

                                                                                                                    gTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAACCCATATGTACt     <  2:1002534/139‑1 (MQ=255)

                                                                                                                       aaTCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCAAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAACCCATATGTACTccc  <  2:345441/139‑1 (MQ=255)

ACCCATAGCTACCTCATTCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATATACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAACCCATATGTACTCCC  >  NC_000913/2796781‑2797038

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A