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
A40 F60 I1 R1	9	40.6	1391456	98.8%	1374758	139.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,815,883	+C	coding (667/687 nt)	rph ←	truncated RNase PH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,815,879	1	.	C	100.0%	118.3 / NA	34	E224G (GAA→GGA)	rph	truncated RNase PH
Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (13/21); total (13/21)

TCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TT‑CCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCT  >  NC_000913/3815740‑3816001

tCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGgattcga‑tt                                                                                                                               <  2:16896/140‑1 (MQ=255)

 cAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGgattcga‑tt‑c                                                                                                                             <  2:522039/140‑1 (MQ=255)

          ggCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCggg                                                                                                                     >  2:106989/1‑140 (MQ=255)

            cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGcc                                                                                                                   >  1:548118/1‑140 (MQ=255)

                  tatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGCCAAAAAAAAGGCGACGCATCAGTCGACTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGcc                                                                                                             <  1:159404/140‑1 (MQ=255)

                   atGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCca                                                                                                            <  1:689668/140‑1 (MQ=255)

                     ggTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCcaac                                                                                                          >  2:54521/1‑140 (MQ=255)

                      gTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCa                                                                                                                  <  1:526682/131‑1 (MQ=255)

                      gTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCa                                                                                                                  >  2:526682/1‑131 (MQ=255)

                           aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGGGTCGCTACAATGTATTCGA‑TTCCCCCTCGGTCCAGAGCCAACAAGAT‑‑g                                                                                                  >  2:228294/1‑140 (MQ=255)

                            tGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑Ga                                                                                                 <  1:537534/140‑1 (MQ=255)

                             gCCTTCGCTCCTCATCTTACTTTTCGACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAg                                                                                                <  1:295810/140‑1 (MQ=255)

                                                    tCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCt                                                                         >  1:357774/1‑140 (MQ=255)

                                                      tACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGAGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGCGAACGGCTCg                                                                       >  2:70356/1‑140 (MQ=255)

                                                        agaaacaaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGAAGCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGcc                                                                     <  1:167270/134‑1 (MQ=255)

                                                             aaaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTg                                                                <  1:456881/140‑1 (MQ=255)

                                                                    aGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTccc                                                         <  2:53211/140‑1 (MQ=255)

                                                                       cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                      <  2:508576/140‑1 (MQ=255)

                                                                       cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                      <  1:36854/140‑1 (MQ=255)

                                                                       cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                      <  2:397376/140‑1 (MQ=255)

                                                                                     ccTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGATGAGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatgat                                          >  1:585411/1‑140 (MQ=255)

                                                                                      cTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcg                                       <  1:574273/140‑1 (MQ=255)

                                                                                             aTCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCt                                <  2:30626/140‑1 (MQ=255)

                                                                                              tCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCtt                               <  1:106989/140‑1 (MQ=255)

                                                                                              tCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCtt                               <  1:143839/140‑1 (MQ=255)

                                                                                                aGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg                             >  2:9011/1‑140 (MQ=255)

                                                                                                     gCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcat                        <  2:548118/140‑1 (MQ=255)

                                                                                                        aGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCAc                     <  1:679395/140‑1 (MQ=255)

                                                                                                        aGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCAc                     <  1:54521/140‑1 (MQ=255)

                                                                                                         gcgcCGCCTTCTGCGTCTCTACAATGGATTCTAGTT‑CCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTTGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACt                    <  2:301778/140‑1 (MQ=255)

                                                                                                               ccTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACt                    <  1:689829/134‑1 (MQ=255)

                                                                                                               ccTTCTGCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACt                    >  2:689829/1‑134 (MQ=255)

                                                                                                                     gCGTCGCTACAATGGATTCGA‑TTCCCCCTCGTGCCTGAGGCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCg        <  2:318008/140‑1 (MQ=255)

                                                                                                                     gCGTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCATGCACTTCCATGATACACCCGTCTTTGGTCACCACTACGGTCATGTCg        >  2:332101/1‑140 (MQ=255)

                                                                                                                       gTCGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt      <  2:57684/140‑1 (MQ=255)

                                                                                                                         cGCTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGtct    >  1:135504/1‑140 (MQ=255)

                                                                                                                           cTACAATGGATTCGA‑TTCCCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTctct  >  1:83412/1‑140 (MQ=255)

TCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TT‑CCCCTCGGGCCAGAGCCAACAAGAT‑‑GAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCT  >  NC_000913/3815740‑3816001

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A