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
A6 F1 I1 R1	750	51.0	2595496	93.6%	2429384	106.4

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%	137.2 / NA	38	Y38C (TAT→TGT)	yqaE	cyaR sRNA‑regulated protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (18/20); total (18/20)

TAGCTACCTCATTCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATATACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAACCCATATGTACT  >  NC_000913/2796786‑2797035

tAGCTACCTCATTCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGc                                                                                                                 <  1:256146/139‑1 (MQ=255)

 aGCTACCTCATTCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCa                                                                                                                <  2:593294/139‑1 (MQ=255)

        tCATTCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCaa                                                                                                         <  1:246958/139‑1 (MQ=255)

           ttCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAg                                                                                                      >  2:27777/1‑139 (MQ=255)

             cGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGaa                                                                                                    >  1:288046/1‑139 (MQ=255)

                                 aaGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCaa                                                                                <  2:288046/139‑1 (MQ=255)

                                    tgtAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGcc                                                                                   >  2:280823/1‑133 (MQ=255)

                                    tgtAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGcc                                                                                   <  1:280823/133‑1 (MQ=255)

                                    tgtAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCg                                                                             >  2:697101/1‑139 (MQ=255)

                                    tgtAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCg                                                                             <  2:1179764/139‑1 (MQ=255)

                                                   cggcgCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGc                                                                                                                 <  1:538210/88‑1 (MQ=255)

                                                   cggcgCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGc                                                                                                                 >  2:538210/1‑88 (MQ=255)

                                                   cggcgCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGagc                                                              <  1:27777/139‑1 (MQ=255)

                                                   cggcgCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGagc                                                              >  1:815596/1‑139 (MQ=255)

                                                        cgTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAAc                                                                                                        >  1:354065/1‑92 (MQ=255)

                                                        cgTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAAc                                                                                                        <  2:354065/92‑1 (MQ=255)

                                                                    ggggATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGcggcgg                                             <  2:815596/139‑1 (MQ=255)

                                                                     gggATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCg                                                                             <  1:609504/106‑1 (MQ=255)

                                                                     gggATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCg                                                                             >  2:609504/1‑106 (MQ=255)

                                                                         tGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCaa                                                                                                                   <  2:1140469/64‑1 (MQ=255)

                                                                         tGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCaa                                                                                                                   >  1:1140469/1‑64 (MQ=255)

                                                                         tGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACC‑GGGATACACCCaa                                                                                                                   >  1:916178/1‑63 (MQ=255)

                                                                         tGAGCACAGGTTTAATCGAGGGTTTGCACCCAGAACGCGTGAATCAAACC‑GGGATACACCCaa                                                                                                                   <  2:916178/63‑1 (MQ=255)

                                                                                  ggttAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAAc                                                                                                        >  2:776603/3‑66 (MQ=255)

                                                                                  gTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAAc                                                                                                        <  1:776603/66‑1 (MQ=255)

                                                                                       aTCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGc                                                                                                                 >  2:1198747/1‑52 (MQ=255)

                                                                                       aTCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGc                                                                                                                 <  1:1198747/52‑1 (MQ=255)

                                                                                       aTCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCaa                                                                                                         >  2:177753/1‑60 (MQ=255)

                                                                                       aTCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCaa                                                                                                         <  1:177753/60‑1 (MQ=255)

                                                                                           cgGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATtc                      >  1:214522/1‑139 (MQ=255)

                                                                                            gggTTTGCACCCATAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAgcgg                                                <  2:814788/112‑1 (MQ=255)

                                                                                            gggTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAg                                                                                                      <  2:141091/58‑1 (MQ=255)

                                                                                            gggTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAg                                                                                                      >  1:141091/1‑58 (MQ=255)

                                                                                            gggTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAgcgg                                                >  1:814788/1‑112 (MQ=255)

                                                                                                     cccAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAAcc            <  2:214522/139‑1 (MQ=255)

                                                                                                               gTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAACCCATATGTACt  >  1:8395/1‑139 (MQ=255)

                                                                                                                tGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAg                                                                                                      >  2:33096/1‑38 (MQ=255)

                                                                                                                tGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAg                                                                                                      <  1:33096/38‑1 (MQ=255)

TAGCTACCTCATTCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATATACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAACCCATATGTACT  >  NC_000913/2796786‑2797035

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 28 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A