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
A12 F28 I1 R1	123	51.0	1731148	99.3%	1719029	138.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,871,475	T→C	A102A (GCA→GCG)	ispF ←	2‑C‑methyl‑D‑erythritol 2,4‑cyclodiphosphate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,871,475	0	T	C	100.0%	120.2 / NA	33	A102A (GCA→GCG)	ispF	2‑C‑methyl‑D‑erythritol 2,4‑cyclodiphosphate synthase
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (18/15); total (18/15)

GGCAATCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTCCGTAGTAGTGGCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCTTCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGTGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGTATAACCCTTCGCCTGAATACGACGCCAGGCTTCGCGTAGCAGCTCGCGGCTATCGGCACCTTTAAATGCCGGATCGGTATCCGGGAACAG  >  NC_000913/2871340‑2871603

ggCAATCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTCCGTAGTAGTGGCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCTTCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCt                                                                                                                              >  1:640354/1‑140 (MQ=255)

   aaTCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTCCGTAGTAGTGGCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCTTCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGAg                                                                                                                           <  2:41013/140‑1 (MQ=255)

   aaTCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTCCGTAGTAGTGGCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCTTCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGAg                                                                                                                           <  1:807676/140‑1 (MQ=255)

    aTCCCTTCCCCATGTCCGGTAAATCCCAGTTTTTCCGTAGTAGTGGCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCTTCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGAGc                                                                                                                          >  1:740713/1‑140 (MQ=255)

    aTCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTCCGTAGTAGTGGCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCTTCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGAGc                                                                                                                          >  2:562376/1‑140 (MQ=255)

     tCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTCCGTAGTAGTGGCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCTTCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGAGCg                                                                                                                         <  1:156374/140‑1 (MQ=255)

                   ccGGTAAATCCCAGTTTTTCCGTAGTAGTGGCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCTTCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGa                                                                                                                            <  2:67868/123‑1 (MQ=255)

                   ccGGTAAATCCCAGTTTTTCCGTAGTAGTGGCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCTTCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGa                                                                                                                            >  1:67868/1‑123 (MQ=255)

                              cAGTTTTTCCGTAGTAGTGGCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCTTCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCaa                                                                                                <  1:85871/140‑1 (MQ=255)

                              cAGTTTTTCCGTAGTAGTGGCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCTTCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCaa                                                                                                <  1:530259/140‑1 (MQ=255)

                                 tttttCCGTAGTAGTGGCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCTTCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCAAggg                                                                                             <  1:417739/140‑1 (MQ=255)

                                           gtagtGGCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCTTCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGtat                                                                                          >  1:598214/1‑133 (MQ=255)

                                           gtagtGGCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCTTCGGCAATAAACACGCGCATTTGTGGAACGTGCGGCAACATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGtat                                                                                          <  2:598214/133‑1 (MQ=255)

                                              gtGGCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCTTCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGTATAACCCTTCGc                                                                                >  2:683524/1‑140 (MQ=255)

                                                 gCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCTTCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGtat                                                                                          <  1:689061/127‑1 (MQ=255)

                                                 gCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCTTCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGtat                                                                                          >  2:689061/1‑127 (MQ=255)

                                                 gCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCTTCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGTATAACCCTTCGCCTg                                                                             >  1:162754/1‑140 (MQ=255)

                                                        cGTTAACATCATCCATATGGCAGCCGAGATCTTCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGTATAACCCTTCGCCTGAATacga                                                                      >  1:820134/1‑140 (MQ=255)

                                                        cGTTAACATCATCCATATGGCAGCCGAGATCTTCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGTATAACCCTTCGCCTGAATacga                                                                      >  1:850987/1‑140 (MQ=255)

                                                                              gCCGAGATCTTCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGTATAACCCTTCGCCTGAATACGACGCCAGGCTTCGCGTAGCAGCt                                                >  1:842384/1‑140 (MQ=255)

                                                                               ccGAGATCTTCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGTATAACCCTTCGCCTGAATACGACGCCAGGCTTCGCGTAGCAGCTc                                               >  1:456940/1‑140 (MQ=255)

                                                                                       ttCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGTATAACCCTTCGCCTGAATACGACGCCAGGCTTCGCGTAGCAGCTCGCGGCTAt                                       >  1:815232/1‑140 (MQ=255)

                                                                                          ggCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGTATAACCCTTCGCCTGAATACGACGCCAGGCTTCGCGTAGCAGCTCGCGGCTATCgg                                    <  2:850987/140‑1 (MQ=255)

                                                                                          ggCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGTATAACCCTTCGCCTGAATACGACGCCAGGCTTCGCGTAGCAGCTCGCGGCTATCgg                                    <  2:86785/140‑1 (MQ=255)

                                                                                                       cgcATTTGTGGAATGTGCGGCAACATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGTATAACCCTTCGCCTGAATACGACGCCAGGCTTCGCGTAGCAGCTCGCGGCTATCGGCACCTTTAAATGc                       <  2:84017/140‑1 (MQ=255)

                                                                                                                      tgCGGCAACATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGTATAACCCTTCGCCTGAATACGACGCCAGGCTTCGCGTAGCAGCTCGCGGCTATCGGCACCTTTAAATGCCGGATCGGTATCTgg        >  1:188337/1‑140 (MQ=255)

                                                                                                                      tgCGGCAACATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGTATAACCCTTCGCCTGAATACGACGCCAGGCTTCGCGTAGCAGCTCGCGGCTATCGGCACCTTTAAATGCCGGATCGGTATCCgg        >  2:161984/1‑140 (MQ=255)

                                                                                                                      tgCGGCAACATCTTCGGCACCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGTATAACCCTTCGCCTGAATACGACGCCAGGCTTCGCGTAGCAGCTCGCGGCTATCGGCACCTTTAAATGCCGGATCGGTATCCgg        >  1:200859/1‑140 (MQ=255)

                                                                                                                        cGGCAACATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGTATAACCCTTCGCCTGAATACGACGCCAGGCTTCGCGTAGCAGCTCGCGGCTATCGGCACCTTTAAATGCCGGATCGGTATCCGGGa      >  1:792664/1‑140 (MQ=255)

                                                                                                                            aaCATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGTATAACCCTTCGCCTGAATACGACGCCAGGCTTCGCGTAGCAGCTCGCGGCTATCGGCACCTTTAAATGCCGGATCGGTATCCGGGAACAg  <  1:623145/140‑1 (MQ=255)

                                                                                                                            aaCATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGTATAACCCTTCGCCTGAATACGACGCCAGGCTTCGCGTAGCAGCTCGCGGCTATCGGCACCTTTAAATGCCGGATCGGTATCCGGGAACAg  <  2:842384/140‑1 (MQ=255)

                                                                                                                              cATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGTATAACCCTTCGCCTGAATACGACGCCAGGCTTCGCGTAGCAGCTCGCGGCTATCGGCACCTTTAAATGCCGGATc                 <  1:776624/123‑1 (MQ=255)

                                                                                                                              cATCTTCGGCGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGTATAACCCTTCGCCTGAATACGACGCCAGGCTTCGCGTAGCAGCTCGCGGCTATCGGCACCTTTAAATGCCGGATc                 >  2:776624/1‑123 (MQ=255)

GGCAATCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTCCGTAGTAGTGGCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCTTCGGCAATAAACACGCGCATTTGTGGAATGTGCGGCAACATCTTCGGTGCCTGAGCGATGATAGTGACATCGACGTTGCCAAGGGTATAACCCTTCGCCTGAATACGACGCCAGGCTTCGCGTAGCAGCTCGCGGCTATCGGCACCTTTAAATGCCGGATCGGTATCCGGGAACAG  >  NC_000913/2871340‑2871603

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A