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
A2 F5 I184 R1	278	29.6	1166432	97.3%	1134938	124.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	791,624	T→C	S103P (TCG→CCG)	modB →	molybdate ABC transporter permease subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	791,624	0	T	C	96.5%	90.5 / ‑3.2	29	S103P (TCG→CCG)	modB	molybdate ABC transporter permease subunit
Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (14/14); total (15/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.54e-01

ACCGCCCGTGGTCGTCGGTTACTTATTATTAGTTTCGATGGGACGGCGCGGATTTATCGGTGAACGTCTGTATGACTGGTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGTCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGGCGCGTTTTCTTTACTATCACGTTACCGCTGACCTTACC  >  NZ_CP009273/791488‑791757

aCCGCCCGTGGTCGTCGGTTACTTATTATTAGTTTCGATGGGACGGCGCGGATTTATCGGTGAACGTCTGTATGACTGGTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCg                                                                                                                                     >  1:452202/1‑139 (MQ=255)

              tcgGTTACTTATTATTAGTTTCGATGGGACGGCGCGGATTTATCGGTGAACGTCTGTATGACTGGTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGt                                                                                                                       <  2:78143/139‑1 (MQ=255)

                ggTTACTTATTATTAGTTTCGATGGGACGGCGCGGATTTATCGGTGAACGTCTGTATGACTGGTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTg                                                                                                                      <  1:65755/138‑1 (MQ=255)

                            ttaGTTTCGATGGGACGGCGCGGATTTATCGGTGAACGTCTGTATGACTGGTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTc                                                                                                         <  1:36143/139‑1 (MQ=255)

                                  tCGATGGGACGGCGCGGATTTATCGGTGAACGTCTGTATGACTGGTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGgcg                                                                                                    <  1:464313/138‑1 (MQ=255)

                                    gATGGGACGGCGCGGATTTATCGGTGAACGTCTGTATGACTGGTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCACGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTg                                                                                                 >  2:400502/1‑139 (MQ=255)

                                      tGGGACGGCGCGGATTTATCGGTGAACGTCTGTATGACTGGTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGa                                                                                               <  1:402197/139‑1 (MQ=255)

                                            ggCGCGGATTTATCGGTGAACGTCTGTATGACTGGTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGt                                                                                         <  2:243228/139‑1 (MQ=255)

                                              cgcgGATTTATCGGTGAACGTCTGTATGACTGGTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGtt                                                                                        >  1:210234/1‑138 (MQ=255)

                                                                      tATGACTGGTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGc                                                                 >  2:92963/1‑137 (MQ=255)

                                                                        tggcTGGTGTGGTATTACCTTCGCCTTTAGCTGGAGCGGCGCAGTTCTCGATGCCGCAGTGACGCCGTTTCCGCTGATGGTGCGGGCAATACGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGa                                                             <  2:236854/136‑1 (MQ=255)

                                                                              gTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTg                                                       >  2:538365/1‑139 (MQ=255)

                                                                                ttGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTggg                                                     >  2:570110/1‑139 (MQ=255)

                                                                                        aCCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGgc                                             >  1:536978/1‑139 (MQ=255)

                                                                                        aCCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGgc                                             >  1:507596/1‑139 (MQ=255)

                                                                                             cGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTgg                                        >  1:131387/1‑139 (MQ=255)

                                                                                              gCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGgc                                       >  2:302151/1‑139 (MQ=255)

                                                                                                cTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGgcgc                                     <  2:210234/139‑1 (MQ=255)

                                                                                                         gcgcggcgcgGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGGCGCGTTTTCt                              <  1:538365/137‑1 (MQ=255)

                                                                                                              gcgcggTTCTCGCTGCCGCCGTCATGCCGTTTCCGCGGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGGCGCGTTTTCTTTACTAt                       <  2:429522/139‑1 (MQ=255)

                                                                                                                          cTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGGCGCGTTTTCTTTACTATCACGTTACCGCt           <  1:92963/139‑1 (MQ=255)

                                                                                                                              cgccgTCATGTCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGGCGCGTTTTCTTTACTATCACGTTACCGCTGAcc       >  2:536867/1‑139 (MQ=255)

                                                                                                                              cgccgTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGGCGCGTTTTCTTTACTATCACGTTACCGCTGAcc       >  2:489198/1‑139 (MQ=255)

                                                                                                                              cgccgTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGGCGCGTTTTCTTTACTATCACGTTACCGCTGAcc       >  2:536465/1‑139 (MQ=255)

                                                                                                                                ccgTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGGCGCGTTTTCt                              <  2:183495/114‑1 (MQ=255)

                                                                                                                                ccgTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGGCGCGTTTTCt                              >  1:183495/1‑114 (MQ=255)

                                                                                                                                   tCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGGCGCGTTTTCt                              <  2:226757/111‑1 (MQ=255)

                                                                                                                                   tCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGGCGCGTTTTCt                              >  1:226757/1‑111 (MQ=255)

                                                                                                                                   tCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGGCGCGTTTTCTTTACTATCACGTTACCGCTGACCTTAcc  <  1:216971/139‑1 (MQ=255)

ACCGCCCGTGGTCGTCGGTTACTTATTATTAGTTTCGATGGGACGGCGCGGATTTATCGGTGAACGTCTGTATGACTGGTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGTCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGGCGCGTTTTCTTTACTATCACGTTACCGCTGACCTTACC  >  NZ_CP009273/791488‑791757

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

CCGCTGGTGTTACCGCCCGTGGTCGTCGGTTACTTATTATTAGTTTCGATGGGACGGCGCGGATTTATCGGTGAACGTCTGTATGACTGGTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGTCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGGCGCGTTTTCTTTACTATCACGTTACCGCTGACCTTACCGGGAATTATTG  >  NZ_CP009273/791477‑791768

CCGCTGGTGTTACCGCCCGTGGTCGTCGGTTACTTATTATTAGTTTCGATGGGACGGCGCGGATTTATCGGTGAACGTCTGTATGACTGGTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGT                                                                                                                                               >  SRR3722139.457492/1‑151 (MQ=60)

                          CGGTTACTTATTATTAGTTGCGATGGGACGGCGCGGATTTATCGGTGAACGTCTGTATGACTGGTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCG                                                                                                                      <  SRR3722139.66543/150‑1 (MQ=60)

                                      ATTAGTTTCGATGGGACGGCGCGGATTTATCGGTGAACGTCTGTATGACTGGTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAA                                                                                                         <  SRR3722139.36532/151‑1 (MQ=60)

                                            TTCGATGGGACGGCGCGGATTTATCGGTGAACGTCTGTATGACTGGTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGT                                                                                                    <  SRR3722139.469747/150‑1 (MQ=60)

                                              CGATGGGACGGCGCGGATTTATCGGTGAACGTCTGTATGACTGGTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTG                                                                                                  >  SRR3722139.212841/1‑150 (MQ=60)

                                                ATGGGACGGCGCGGATTTATCGGTGAACGTCTGTATGACTGGTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATG                                                                                               <  SRR3722139.406965/151‑1 (MQ=60)

                                                                                        GGTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCG                                                       >  SRR3722139.513444/1‑151 (MQ=60)

                                                                                        GGTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCG                                                       >  SRR3722139.543142/1‑151 (MQ=60)

                                                                                             GGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGGC                                                  >  SRR3722139.132995/1‑151 (MQ=60)

                                                                                                                   GGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGGCGCGTTTTCTTTACTATCACG                              <  SRR3722139.544540/149‑1 (MQ=60)

                                                                                                                                TCTCGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGGCGCGTTTTCTTTACTATCACGctgtctcttatacac               >  SRR3722139.185763/1‑136 (MQ=60)

                                                                                                                                   CGCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGGCGCGTTTTCTTTACTATCACGctgtctcttatacacatc            >  SRR3722139.229561/1‑133 (MQ=60)

                                                                                                                                    GCTGCCGCCGTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGGCGCGTTTTCTTTACTATCACGTTACCGCTGACCTTACCGG           <  SRR3722139.94071/151‑1 (MQ=60)

                                                                                                                                             GTCATGCCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGGCGCGTTTTCTTTACTATCACGTTACCGCTGACCTTACCGGGAATTATTG  <  SRR3722139.219633/151‑1 (MQ=60)

CCGCTGGTGTTACCGCCCGTGGTCGTCGGTTACTTATTATTAGTTTCGATGGGACGGCGCGGATTTATCGGTGAACGTCTGTATGACTGGTTTGGTATTACCTTCGCCTTTAGCTGGCGCGGCGCGGTTCTCGCTGCCGCCGTCATGTCGTTTCCGCTGATGGTGCGGGCAATTCGTCTGGCGCTGGAAGGGGTTGATGTCAAACTGGAACAGGCCGCAAGAACACTGGGGGCCGGGCGCTGGCGCGTTTTCTTTACTATCACGTTACCGCTGACCTTACCGGGAATTATTG  >  NZ_CP009273/791477‑791768

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`