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 I181 R1	159	32.7	1279082	96.9%	1239430	121.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	438,112	A→G	S370G (AGC→GGC)	thiI →	tRNA 4‑thiouridine(8) synthase ThiI

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	438,112	0	A	G	100.0%	115.0 / NA	31	S370G (AGC→GGC)	thiI	tRNA 4‑thiouridine(8) synthase ThiI
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (16/15); total (16/15)

CAACCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCAGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGAT  >  NZ_CP009273/437979‑438240

caACCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCAtt                                                                                                                             >  2:223396/1‑139 (MQ=255)

 aaCCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCAtt                                                                                                                             <  1:147533/138‑1 (MQ=255)

        cccGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATa                                                                                                                      >  1:459673/1‑138 (MQ=255)

                   ggCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAg                                                                                                           <  1:244316/138‑1 (MQ=255)

                          aaGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGaa                                                                                                   <  2:351013/139‑1 (MQ=255)

                          aaGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGaa                                                                                                   >  1:217791/1‑139 (MQ=255)

                                  gCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCAt                                                                                                                              >  1:214964/1‑104 (MQ=255)

                                  gCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCAt                                                                                                                              <  2:214964/104‑1 (MQ=255)

                                              ccGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGaaa                                                                               <  1:187907/139‑1 (MQ=255)

                                                           gtgtGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATa                                                                                                 <  2:636389/108‑1 (MQ=255)

                                                           gtgtGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATa                                                                                                 >  1:636389/1‑108 (MQ=255)

                                                            tgtgATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCg                                                                            <  2:208668/128‑1 (MQ=255)

                                                            tgtgATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCg                                                                            >  1:208668/1‑128 (MQ=255)

                                                              tgATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGAcc                                                                 >  2:388980/1‑137 (MQ=255)

                                                                aTCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAg                                                              >  2:288887/1‑138 (MQ=255)

                                                                 tctcCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCAtt                                                                                                                             <  1:419585/74‑1 (MQ=255)

                                                                 tctcCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCAtt                                                                                                                             >  2:419585/1‑74 (MQ=255)

                                                                   tcCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGaa                                                                                                   >  1:192387/1‑98 (MQ=255)

                                                                   tcCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGaa                                                                                                   <  2:192387/98‑1 (MQ=255)

                                                                             cGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGtggtgg                                                 >  1:104260/1‑138 (MQ=255)

                                                                                                 tCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCt                            <  2:217791/139‑1 (MQ=255)

                                                                                                    aaGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCg                         >  1:365898/1‑139 (MQ=255)

                                                                                                    aaGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCg                         >  2:473906/1‑139 (MQ=255)

                                                                                                      gATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAgtggtg                                                  >  1:60281/1‑112 (MQ=255)

                                                                                                      gATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAgtggtg                                                  <  2:60281/112‑1 (MQ=255)

                                                                                                           aaGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCACGa                   <  2:547332/138‑1 (MQ=255)

                                                                                                                 aagaagAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGAcc                                                                 >  2:586626/1‑86 (MQ=255)

                                                                                                                 aagaagAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGAcc                                                                 <  1:586626/86‑1 (MQ=255)

                                                                                                                           gTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGat  <  1:588721/139‑1 (MQ=255)

                                                                                                                                 cTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGaa                  <  1:326559/117‑1 (MQ=255)

                                                                                                                                 cTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGaa                  >  2:326559/1‑117 (MQ=255)

CAACCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCAGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGAT  >  NZ_CP009273/437979‑438240

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `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

CATCAACCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCAGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGATATCCGTTCTATCGATGAAC  >  NZ_CP009273/437976‑438259

CATCAACCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAA                                                                                                                                        >  SRR3722135.465915/1‑150 (MQ=60)

  cggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagTTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGT                                                                                                                                     <  SRR3722135.425339/96‑1 (MQ=60)

   CAACCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGT                                                                                                                                     <  SRR3722135.149595/150‑1 (MQ=60)

                  GATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAAT                                                                                                                     >  SRR3722135.220862/1‑151 (MQ=60)

                     TGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAA                                                                                                                   <  SRR3722135.247781/150‑1 (MQ=60)

                          CCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGctgtctcttatacacatctccgagc                                                                                                             >  SRR3722135.218000/1‑126 (MQ=60)

                                                GCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAG                                                                                       <  SRR3722135.190581/151‑1 (MQ=60)

                                                   GGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCtgtctcttatacacatctcc                                                                                    >  SRR3722135.644657/1‑131 (MQ=60)

                                                    GAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCC                                                                                   >  SRR3722135.211594/1‑151 (MQ=60)

                                                           GTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATActgtctcttatacacatctccgagcccacg                                                                             >  SRR3722135.195113/1‑120 (MQ=60)

                                                                 agtacggtctcgtgggctcggagatgtgtataagagacagGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGT                                                                         <  SRR3722135.594319/108‑1 (MQ=60)

                                                                     CTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGA                                                                   >  SRR3722135.105690/1‑150 (MQ=60)

                                                                                            CAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGG                                           >  SRR3722135.371051/1‑151 (MQ=60)

                                                                                              GTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCtgtctcttatacacat                                         >  SRR3722135.61081/1‑135 (MQ=60)

                                                                                                              ataagagacagGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCC                          <  SRR3722135.331224/139‑1 (MQ=60)

                                                                                                                             AGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGATATCCGTTCTAT          <  SRR3722135.596429/151‑1 (MQ=60)

                                                                                                                              GTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGATATCCGTTCTATC         >  SRR3722135.396321/1‑151 (MQ=60)

                                                                                                                                      TCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGATATCCGTTCTATCGATGAAC  <  SRR3722135.91179/150‑1 (MQ=60)

CATCAACCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCAGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGATATCCGTTCTATCGATGAAC  >  NZ_CP009273/437976‑438259

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`