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
A13 F1 I2 R1	92	50.6	2362856	94.3%	2228173	111.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,090,709	C→T	D73N (GAC→AAC)	frvX ←	putative peptidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,090,709	0	C	T	100.0%	130.4 / NA	38	D73N (GAC→AAC)	frvX	putative peptidase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (18/20); total (18/20)

CGCGACGGAACCAATCACACCAGGGATTTTCACTCCCTTGTGTGTGCGTATGGTTACCCGGTGGTTGAGCATCGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTCGATGTGGGTGACCATAAAGCCGACTTCATCCATATGTCCGACAACGGCAACTTTTGGACCTTTATTCCCCTTACGGGCAACAAAGCTGCCCAGACCATCGAAGGTGATTTCATTCACGCAAGGTTCCAGCGTG  >  NC_000913/4090584‑4090842

cgcgACGGAACCAATCACACCAGGGATTTTCACTCCCTTGTGTGTGCGTATGGTTACCCGGTGGTTGAGCATCGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGAcc                                                                                                                          <  1:302881/139‑1 (MQ=255)

          ccAATCACACCAGGGATTTTCACTCCCTTGTGTGTGCGTATGGTTACCCGGTGGTTGAGCATCGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGa                                                                                                                <  1:1119798/139‑1 (MQ=255)

            aaTCACACCAGGGATTTTCACTCCCTTGTGTGTGCGTATGGTTACCCGGTGGTTGAGCATCGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACt                                                                                                              <  1:1061723/139‑1 (MQ=255)

                   ccAGGGATTTTCACTCCCTTGTGTGTGCGTATGGTTACCCGGTGGTTGAGCATCGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCa                                                                                                       <  2:80437/139‑1 (MQ=255)

                   ccAGGGATTTTCACTCCCTTGTGTGTGCGTATGGTTACCCGGTGGTTGAGCA‑CGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCat                                                                                                      <  2:1000769/139‑1 (MQ=255)

                    cAGGGATTTTCACTCCCTTGTGTGTGCGTATGGTTACCCGGTGGTTGAGCATCGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCat                                                                                                      >  1:996022/1‑139 (MQ=255)

                       ggATTTTCACTCCCTTGTGTGTGCGTATGGTTACCCGGTGGTTGAGCATCGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCATATg                                                                                                   >  2:533353/1‑139 (MQ=255)

                            ttCACTCCCTTGTGTGTGCGTATGGTTACCCGGTGGTTGAGCATCGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCATATGTCCGa                                                                                              >  1:300937/1‑139 (MQ=255)

                                   ccTTGTGTGTGCGTATGGTTACCCGGTGGTTGAGCATCGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCATATGTCCGACAACGGc                                                                                       <  1:520616/139‑1 (MQ=255)

                                           gtgCGTATGGTTACCCGGTGGTTGAGCATCGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCATATGTCCGACAACGGCAACTTTTg                                                                               <  1:533353/139‑1 (MQ=255)

                                             gCGTATGGTTACCCGGTGGTTGAGCATCGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTgg                                                                                                                                <  2:921973/88‑1 (MQ=255)

                                             gCGTATGGTTACCCGGTGGTTGAGCATCGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTgg                                                                                                                                >  1:921973/1‑88 (MQ=255)

                                              cGTATGGTTACCCGGTGGTTGAGCATCGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCa                                                                                                       >  2:868535/1‑112 (MQ=255)

                                              cGTATGGTTACCCGGTGGTTGAGCATCGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCa                                                                                                       <  1:868535/112‑1 (MQ=255)

                                                        cccGGTGGTTGAGCATCGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCATATGTCCGACAACGGCAACTTTTGGACCTTTATTccc                                                                  >  1:950522/1‑139 (MQ=255)

                                                         ccGGTGGTTGAGCATCGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCATATGTCCGACAACGGCAACTTTTGGACCTTTATTcccc                                                                 >  2:464101/1‑139 (MQ=255)

                                                                   aGCATCGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAGGCCGACTTCa                                                                                                           >  1:845503/1‑87 (MQ=255)

                                                                   aGCATCGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCa                                                                                                           <  2:845503/87‑1 (MQ=255)

                                                                   aGCATCGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCATATGTCCGACAACGGCAACTTTTGGACCTTTATTCCCCTTACGGGcaa                                                       <  2:300937/139‑1 (MQ=255)

                                                                       tCGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGa                                                                                                                >  1:1144690/1‑78 (MQ=255)

                                                                       tCGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGa                                                                                                                <  2:1144690/78‑1 (MQ=255)

                                                                               ttCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATcc                                                                                                        <  1:792253/78‑1 (MQ=255)

                                                                               ttCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATcc                                                                                                        >  2:792253/1‑78 (MQ=255)

                                                                                        ccgccAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCATATGTCCGACAACGGCAACTTTTGGACCTTTATTCCCCTTACGGGCAACAAAGCTGCCCAGACCATCGa                                  >  2:6744/1‑139 (MQ=255)

                                                                                          gccAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCATATGTCCGACAACGGCAACTTTTgg                                                                              >  1:532559/1‑93 (MQ=255)

                                                                                          gccAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCATATGTCCGACAACGGCAACTTTTgg                                                                              <  2:532559/93‑1 (MQ=255)

                                                                                          gccAATGGTGGTAAAACGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCATATGTCCGACAACGGCAACTTTTGGACCTTTATTCCCCTTACGGGCAACAAAGCTGCCCAGACCATCGAAg                                >  1:210629/1‑139 (MQ=255)

                                                                                                      aaaaCGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCATATGTCCGACAACGGCAACTTTTg                                                                               <  2:613557/80‑1 (MQ=255)

                                                                                                      aaaaCGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCATATGTCCGACAACGGCAACTTTTg                                                                               >  1:613557/1‑80 (MQ=255)

                                                                                                          cGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCATATGTCCGACTACGGCAACTTTTg                                                                               <  2:690945/76‑1 (MQ=255)

                                                                                                          cGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCATATGTCCGACAACGGCAACTTTTg                                                                               >  1:690945/1‑76 (MQ=255)

                                                                                                          cGCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCATATGACCGACAACGGCAACTTTTGGACCTTTATTCCCCTTACGGGCAACAAAGCTGCCCAGACCATCGAAGGTGATTTCTTTCACGc                >  2:631955/1‑139 (MQ=255)

                                                                                                           gCAGAAAACCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCATATGTCCGACAACGGCAACTTTTGGACCTTTATTCCCCTTACGGGCAACAAAGCTGCCCAGACCATCGAAGGTGATTTCATTCACGCa               <  2:950522/139‑1 (MQ=255)

                                                                                                                 aaCCGCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCATATGTCCGACAACGGCAACTTTTGGACCTTTATTCCCCTTACGGGCAACAAAGCTGCCCAGACCATCGAAGGTGATTTCATTCACGCAAGGTTc         >  2:107115/1‑139 (MQ=255)

                                                                                                                     gCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCATATGTCCGACAACGGCAACTTTTGGACCTTTATTCCCCTTACGGGCAACAAAGCTGCCCAGACCATCGAAGGTGATTTCATTCACGCAAGGTTCCAGc     <  2:210629/139‑1 (MQ=255)

                                                                                                                     gCTCTCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCATATGTCCGACAACGGCAACTTTTGGACCTTTATTCCCCTTACGGGCAACAAAGCTGCCCAGACCATCGAAGGTGATTTCATTCACGCAAGGTTCCAGc     <  2:1138982/139‑1 (MQ=255)

                                                                                                                      ctctCGTTGATGTGGGTGACCATAAAGCCGACTTCATCCATATGTCCGACAACGGCAACTTTTTGACCTTTATTCCCCTTACGGGCAACAAAGCTGCCCAGAACATCGAAGGTGATTTCATTCACTCAAGGTTCCACCg    >  1:1105000/1‑139 (MQ=255)

                                                                                                                        ctcGTTGATGTGGGTGACCATAAAGCCGACTTCATCCATATGTCCGACAACGGCAACTTTTGGACCTTTATTCCCCTTACGGGCAACAAAGCTGCCCAGACCATCGAAGGTGATTTCATTCACGCAAGGTTCCAGCgtg  <  2:1040423/139‑1 (MQ=255)

CGCGACGGAACCAATCACACCAGGGATTTTCACTCCCTTGTGTGTGCGTATGGTTACCCGGTGGTTGAGCATCGACTGATTCCACCAGCCGCCAATGGTGGTAAAACGCAGAAAACCGCTCTCGTCGATGTGGGTGACCATAAAGCCGACTTCATCCATATGTCCGACAACGGCAACTTTTGGACCTTTATTCCCCTTACGGGCAACAAAGCTGCCCAGACCATCGAAGGTGATTTCATTCACGCAAGGTTCCAGCGTG  >  NC_000913/4090584‑4090842

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