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
A1 F5 I97 R1	275	44.0	1733530	96.5%	1672856	122.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	687,482	C→T	A106T (GCG→ACG)	ybeY ←	rRNA maturation RNase YbeY

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	687,482	0	C	T	80.7%	72.6 / 10.2	31	A106T (GCG→ACG)	ybeY	rRNA maturation RNase YbeY
Reads supporting (aligned to +/- strand): ref base C (6/0); new base T (17/8); total (23/8)
Fisher's exact test for biased strand distribution p-value = 2.98e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.70e-01

ATCCTCATAGCCCAGAGCAAGCATAATCTCTGTTTCGAGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGCCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCAAACGGGAAGGAGAGCACGTTGGTCGGCTTATCCT  >  NZ_CP009273/687354‑687616

aTCCTCATAGCCCAGAGCAAGCATAATCTCTGTTTCGAGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGCCTCCAGTGGt                                                                                                                              >  1:763963/1‑139 (MQ=255)

     cATAGCCCAGAGCAAGCATAATCTCTGTTTCGAGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGcc                                                                                                                         >  1:43702/1‑139 (MQ=255)

     cATAGCCCAGAGCAAGCATAATCTCTGTTTCGAGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGCCTCCAGTGGTTTGcc                                                                                                                         >  2:762594/1‑139 (MQ=255)

               agcaagcaTAATCTCTGTTTCGAGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCt                                                                                                                 >  1:78877/1‑137 (MQ=255)

                  aagcaTAATCTCTGTTTCGAGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGct                                                                                                            <  1:824245/139‑1 (MQ=255)

                      aTAATCTCTGTTTCGAGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGcttcct                                                                                                        <  2:165930/139‑1 (MQ=255)

                        aaTCTCTGTTTCGAGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGcttccttc                                                                                                      >  2:826820/1‑139 (MQ=255)

                               gTTTCGAGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAacca                                                                                               >  2:167860/1‑139 (MQ=255)

                                tttCGAGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAaccac                                                                                              <  1:497955/139‑1 (MQ=255)

                                tttCGAGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAaccac                                                                                              >  2:823254/1‑139 (MQ=255)

                                     aGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGt                                                                                                                              >  1:181347/1‑102 (MQ=255)

                                     aGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGt                                                                                                                              <  2:181347/102‑1 (MQ=255)

                                     aGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGAc                                                                                         >  1:664659/1‑139 (MQ=255)

                                     aGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGAc                                                                                         >  2:19257/1‑139 (MQ=255)

                                     aGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGAc                                                                                         >  2:192778/1‑139 (MQ=255)

                                       ggCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACgg                                                                                       <  1:259626/139‑1 (MQ=255)

                                         cTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCa                                                                                     <  1:826820/139‑1 (MQ=255)

                                                                       tgtgATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTc                                                       >  2:731177/1‑139 (MQ=255)

                                                                          gATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCAt                                                    >  1:143210/1‑139 (MQ=255)

                                                                                     aaCAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCa                                         >  1:702559/1‑139 (MQ=255)

                                                                                           tGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCaa                                   <  2:43702/139‑1 (MQ=255)

                                                                                                   gCCGTGCACCACCATATGCGCCCAGTGCGCCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCCTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCAAACGGGAAg                           >  2:715843/1‑139 (MQ=255)

                                                                                                    ccGGGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCAAACGGGGAg                           >  2:855128/1‑138 (MQ=255)

                                                                                                            caccaTATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCAAACGGGAAGGAGAGCACg                  >  2:450081/1‑139 (MQ=255)

                                                                                                              ccaTATGCGCCCAGTGCGCCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCAAACGGGAAGGAGAGCACGtt                >  1:759722/1‑139 (MQ=255)

                                                                                                                atatGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCAAACGGGAAGGAGAGCACGTTgg              <  2:232277/139‑1 (MQ=255)

                                                                                                                 tatGCGCCCAGTGCGCCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCAAACGGGAAGGAGAGCACGTTGGt             >  1:862927/1‑139 (MQ=255)

                                                                                                                      gcCCAGTGCGTCTCCAGTGGTTTGCCATGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCAAACGGGAAGGAGAGCACGTTGGTCGGCt        >  1:830471/1‑139 (MQ=255)

                                                                                                                         cAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCAAACGGGAAGGAGAGCACGTTGGTCGGCTTAt     >  2:193538/1‑139 (MQ=255)

                                                                                                                         cAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCAAACGGGAAGGAGAGCACGTTGGTCGGCTTAt     >  1:562159/1‑139 (MQ=255)

                                                                                                                            tGCGCCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGCTCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCAAACGGGCAGGAGAGCACGTTGGTCGGCTTATCCt  >  1:713141/1‑139 (MQ=255)

ATCCTCATAGCCCAGAGCAAGCATAATCTCTGTTTCGAGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGCCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCAAACGGGAAGGAGAGCACGTTGGTCGGCTTATCCT  >  NZ_CP009273/687354‑687616

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 36 ≤` `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

CGGCAATGTACGGATCCTCATAGCCCAGAGCAAGCATAATCTCTGTTTCGAGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGCCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCAAACGGGAAGGAGAGCACGTTGGTCGGCTTATCCTTACCGCGATAGGTC  >  NZ_CP009273/687341‑687630

cggagatgtgtataagagacagGCCCAGAGCAAGCATAATCTCTGTTTCGAGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGT                                                                                                                                               <  SRR3722120.366563/127‑1 (MQ=60)

  GCAATGTACGGATCCTCATAGCCCAGAGCAAGCATAATCTCTGTTTCGAGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGCCTCCAGTGGTT                                                                                                                                           >  SRR3722120.774254/1‑151 (MQ=60)

       GTACGGATCCTCATAGCCCAGAGCAAGCATAATCTCTGTTTCGAGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCT                                                                                                                                      >  SRR3722120.44228/1‑151 (MQ=60)

                 TCATAGCCCAGAGCAAGCATAATCTCTGTTTCGAGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTG                                                                                                                              >  SRR3722120.79906/1‑149 (MQ=60)

                              CAAGCATAATCTCTGTTTCGAGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAAC                                                                                                               <  SRR3722120.835326/151‑1 (MQ=60)

                                       TCTCTGTTTCGAGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGtctcttatacacatctccgagccc                                                                                                      >  SRR3722120.183830/1‑127 (MQ=60)

                                       TCTCTGTTTCGAGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACG                                                                                                      >  SRR3722120.673773/1‑151 (MQ=60)

                                            GTTTCGAGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGA                                                                                                 <  SRR3722120.505114/151‑1 (MQ=60)

                                                   GGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATATCCAG                                                                                          <  SRR3722120.263377/151‑1 (MQ=60)

                                                     GCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGAT                                                                                        <  SRR3722120.837939/151‑1 (MQ=60)

                                                                            ATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATG                                                                 >  SRR3722120.145141/1‑151 (MQ=60)

                                                                                       GATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCAC                                                      >  SRR3722120.712138/1‑151 (MQ=60)

                                                                                                                GCCGTGCACCACCATATGCGCCCAGTGCGCCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCAAACGGGAAGGAGAGCACGTTG                             >  SRR3722120.769975/1‑151 (MQ=60)

                                                                                                                   GTGCACCACCATATGCGCCCAGTGCGCCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCAAACGGGAAGGAGAGCACGTTGGTC                          >  SRR3722120.874456/1‑151 (MQ=60)

                                                                                                                        CCACCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCATGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCAAACGGGAAGGAGAGCACGTTGGTCGGCTT                     >  SRR3722120.841631/1‑151 (MQ=60)

                                                                                                                           CCATATGCGCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCAAACGGGAAGGAGAGCACGTTGGTCGGCTTATC                  >  SRR3722120.570028/1‑151 (MQ=60)

                                                                                                                              TATGCGCCCTGTGCGCCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGCTCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCAAACGGGCAGGAGAGCACGTTGGTCGGCTTATCCTT               >  SRR3722120.722866/1‑151 (MQ=60)

                                                                                                                                   GCCCAGTGCGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCAAACGGGAAGGAGAGCACGTTGGTCGGCTTATCCTTACCGC          >  SRR3722120.296615/1‑151 (MQ=60)

                                                                                                                                           CGTCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCAAACGGGAAGGAGAGCACGTTGGTCGGCTTATCCTTACCGCGATAGGTC  <  SRR3722120.70198/151‑1 (MQ=60)

                                                                                                                                             TCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCAAACGGGAAGGAGAGCACGTTGGTCGGCTTATCCTTACCGCGATAGGTC  >  SRR3722120.387305/1‑149 (MQ=60)

CGGCAATGTACGGATCCTCATAGCCCAGAGCAAGCATAATCTCTGTTTCGAGGGCTTCCATTTCTTCTGCTTCGTCATCTTCGATGTGATCGTAACCTAACAAATGCAGACTGCCGTGCACCACCATATGCGCCCAGTGCGCCTCCAGTGGTTTGCCTTGCTCCTGAGCTTCCTTCTCAACCACCTGACGGCAGATAACCAGATCGCCCAGTAGCGACATTTCCATGCCAGGCGGCACTTCAAACGGGAAGGAGAGCACGTTGGTCGGCTTATCCTTACCGCGATAGGTC  >  NZ_CP009273/687341‑687630

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`