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
A25 F36 I0 R2	1302	104.9	4551290	96.3%	4382892	111.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	2,302,452	A→C	7.3%	L101R (CTG→CGG)	napA ←	nitrate reductase, periplasmic, large subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,302,452	0	A	C	7.3%	187.2 / 7.7	55	L101R (CTG→CGG)	napA	nitrate reductase, periplasmic, large subunit
Reads supporting (aligned to +/- strand): ref base A (26/25); new base C (2/2); total (28/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.26e-01

AGGGCGGTTTTGAATTTCTCTTCCATCACATCGAAGGCCTGATCCCAGGTGATTGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTG  >  NC_000913/2302350‑2302573

aGGGCGGTTTTGAATTTCTCTTCCATCACATCGAAGGCCTGATCCCAGGTGATTGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTc                                                                                                        <  4:1096243/122‑1 (MQ=255)

aGGGCGGTTTTGAATTTCTCTTCCATCACATCGAAGGCCTGATCCCAGGTGATTGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTc                                                                                                        >  3:1096243/1‑122 (MQ=255)

        tttGAATTTCTCTTCCATCACATCGAAGGCCTGATCCCAGGTGATTGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAAt                                                                           >  4:152530/1‑143 (MQ=255)

        tttGAATTTCTCTTCCATCACATCGAAGGCCTGATCCCAGGTGATTGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAAt                                                                           <  3:152530/143‑1 (MQ=255)

                   ctTCCATCACATCGAAGGCCTGATCCCAGGTGATTGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGaa                                                                             <  2:66898/130‑1 (MQ=255)

                   ctTCCATCACATCGAAGGCCTGATCCCAGGGGATTGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGaa                                                                             >  1:66898/1‑130 (MQ=255)

                         tCACATCGAAGGCCTGATCCCAGGTGATTGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCCGGcc                                                     >  3:798221/1‑148 (MQ=255)

                           acaTCGAAGGCCTGATCCCAGGTGATTGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCg                                                                                                 >  1:100597/1‑102 (MQ=255)

                           acaTCGAAGGCCTGATCCCAGGTGATTGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCg                                                                                                 <  2:100597/102‑1 (MQ=255)

                            caTCGAAGGCCTGATCCCAGGTGATTGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTa                                                                   <  1:848051/131‑1 (MQ=255)

                            caTCGAAGGCCTGATCCCAGGTGATTGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTa                                                                   >  2:848051/1‑131 (MQ=255)

                                 aaGGCCTGATCCCAGGTGATTGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCg                                                                                                                  >  4:1062169/1‑79 (MQ=255)

                                 aaGGCCTGATCCCAGGTGATTGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCg                                                                                                                  <  3:1062169/79‑1 (MQ=255)

                                     ccTGATCCCAGGTGATTGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCgg                                         <  4:798221/148‑1 (MQ=255)

                                      cTGATCCCAGGTGATTGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCa                                                         <  1:960285/131‑1 (MQ=255)

                                      cTGATCCCAGGTGATTGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCa                                                         >  2:960285/1‑131 (MQ=255)

                                                 tGATTGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTaa                                             >  2:845787/1‑132 (MQ=255)

                                                 tGATTGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTaa                                             <  1:845787/132‑1 (MQ=255)

                                                    ttGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTAc                                                                                                   <  1:212906/75‑1 (MQ=255)

                                                    ttGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTAc                                                                                                   >  2:212906/1‑75 (MQ=255)

                                                     tGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTaa                                                                  <  2:969856/107‑1 (MQ=255)

                                                     tGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTaa                                                                  >  1:969856/1‑107 (MQ=255)

                                                        ggTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTg                                       <  4:385187/131‑1 (MQ=255)

                                                        ggTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTg                                       >  3:385187/1‑131 (MQ=255)

                                                        ggTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCg                                 <  2:235132/137‑1 (MQ=255)

                                                        ggTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCg                                 >  1:235132/1‑137 (MQ=255)

                                                         gTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGAt                                                                                         >  1:854802/1‑80 (MQ=255)

                                                         gTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGAt                                                                                         <  2:854802/80‑1 (MQ=255)

                                                                    ttcttTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTc                                                          >  3:1090363/1‑100 (MQ=255)

                                                                    ttcttTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTc                                                          <  4:1090363/100‑1 (MQ=255)

                                                                    ttcttTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCgg                                         >  3:348008/1‑117 (MQ=255)

                                                                    ttcttTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCgg                                         <  4:348008/117‑1 (MQ=255)

                                                                     tcttTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTc                                                          >  1:411512/1‑99 (MQ=255)

                                                                     tcttTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTc                                                          <  2:411512/99‑1 (MQ=255)

                                                                            cATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCctg  >  1:822973/1‑148 (MQ=255)

                                                                              tatTTACCGTTTTTCATACGCAGCAGCGGCTGCGt                                                                                                                 >  3:1117545/1‑35 (MQ=255)

                                                                              tatTTACCGTTTTTCATACGCAGCAGCGGCTGCGt                                                                                                                 <  4:1117545/35‑1 (MQ=255)

                                                                                tttACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCgg                                         <  1:508647/105‑1 (MQ=255)

                                                                                tttACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCgg                                         >  2:508647/1‑105 (MQ=255)

                                                                                    ccGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTaa                                             <  3:1077960/97‑1 (MQ=255)

                                                                                    ccGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTaa                                             <  3:556276/97‑1 (MQ=255)

                                                                                    ccGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTaa                                             >  4:1077960/1‑97 (MQ=255)

                                                                                    ccGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTaa                                             >  4:556276/1‑97 (MQ=255)

                                                                                        ttttCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGcc                >  3:163016/1‑122 (MQ=255)

                                                                                        ttttCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGcc                <  4:163016/122‑1 (MQ=255)

                                                                                               aCGCAGCCGCTGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGc                                                               >  1:693308/1‑68 (MQ=255)

                                                                                               aCGCAGCCGCTGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGc                                                               <  2:693308/68‑1 (MQ=255)

                                                                                               aCGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAg                                                        <  3:1039280/75‑1 (MQ=255)

                                                                                               aCGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAg                                                        >  4:1039280/1‑75 (MQ=255)

                                                                                               aCGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGc                           <  2:107912/104‑1 (MQ=255)

                                                                                               aCGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGc                           >  1:107912/1‑104 (MQ=255)

                                                                                                cGCAGCCGCTGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCCGTTCAGGCCCCGGTTAACCGGTGCGTCCg                                 >  4:797919/1‑97 (MQ=255)

                                                                                                cGCAGCCGCTGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCg                                 <  3:797919/97‑1 (MQ=255)

                                                                                                cGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCggg                               <  3:758565/99‑1 (MQ=255)

                                                                                                cGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCggg                               >  4:758565/1‑99 (MQ=255)

AGGGCGGTTTTGAATTTCTCTTCCATCACATCGAAGGCCTGATCCCAGGTGATTGGGGTAAATTCGCCTTCTTTGTCATATTTACCGTTTTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTG  >  NC_000913/2302350‑2302573

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A