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	634,477	A→G	E26G (GAA→GGA)	ahpC →	alkyl hydroperoxide reductase subunit C

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	634,477	0	A	G	97.0%	115.3 / NA	33	E26G (GAA→GGA)	ahpC	alkyl hydroperoxide reductase subunit C
Reads supporting (aligned to +/- strand): ref base A (0/0); major base G (14/18); minor base T (0/1); total (14/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCGGCAAAAATTGGTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGAAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTAGACGTATACGCAG  >  NZ_CP009273/634348‑634611

aTCGGCAAAAATTGGTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATAc                                                                                                                               >  1:459070/1‑139 (MQ=255)

    gCAAAAATTGGTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGaa                                                                                                                           <  1:448615/139‑1 (MQ=255)

           ttGGTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCt                                                                                                                    <  2:459070/139‑1 (MQ=255)

              gTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTg                                                                                                                   >  1:434464/1‑137 (MQ=255)

              gTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGa                                                                                                                 <  2:182050/139‑1 (MQ=255)

              gTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGa                                                                                                                 <  2:116177/139‑1 (MQ=255)

                  ccTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCg                                                                                                              <  1:45506/138‑1 (MQ=255)

                      aCATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGtctt                                                                                                          <  1:17914/138‑1 (MQ=255)

                       cATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAACCCTTTTAAAAACCAGACATTCAAACACGGCGAATTCATCGAAATCACCGTAAAAGATACCGAAGGCCGCTGGAGCgtcgtc                                                                                                         <  2:264750/138‑1 (MQ=255)

                             aTCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGtcttcttcttc                                                                                                   >  2:252492/1‑138 (MQ=255)

                             aTCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGtcttcttcttc                                                                                                   >  2:497906/1‑138 (MQ=255)

                                gAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTAcc                                                                                               <  1:411467/139‑1 (MQ=255)

                                  aaaCACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCg                                                                                             <  2:190387/139‑1 (MQ=255)

                                         gaggaAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGact                                                                                      <  1:252492/139‑1 (MQ=255)

                                                       gTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGc                                                                        >  1:331731/1‑139 (MQ=255)

                                                        tCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGcc                                                                       >  2:369039/1‑139 (MQ=255)

                                                          cTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAgg                                                                                                                         <  1:517073/87‑1 (MQ=255)

                                                          cTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAgg                                                                                                                         >  2:517073/1‑87 (MQ=255)

                                                          cTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGccc                                                                      >  2:432343/1‑138 (MQ=255)

                                                          cTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGccc                                                                      >  2:273460/1‑138 (MQ=255)

                                                                  acacCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACt                                                             >  1:575701/1‑139 (MQ=255)

                                                                        aaaTTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGa                                                       >  2:475033/1‑139 (MQ=255)

                                                                        aaaTTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGa                                                       >  1:69638/1‑139 (MQ=255)

                                                                        aaaTTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGa                                                       <  2:331731/139‑1 (MQ=255)

                                                                                    ttAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGAc                                             <  1:273460/137‑1 (MQ=255)

                                                                                         aaCCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACg                                      <  1:4389/139‑1 (MQ=255)

                                                                                             aGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACgaaga                                  <  2:422134/139‑1 (MQ=255)

                                                                                                       aaaCGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGaaa                        <  2:547142/139‑1 (MQ=255)

                                                                                                        aaCGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAAc                       <  2:69638/139‑1 (MQ=255)

                                                                                                          cGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTg                     >  1:553247/1‑139 (MQ=255)

                                                                                                             cGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGc                  >  1:335395/1‑139 (MQ=255)

                                                                                                                aTTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTa               <  1:475033/139‑1 (MQ=255)

                                                                                                                             aCCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTAGACGTATACGCAg  <  1:432343/139‑1 (MQ=255)

ATCGGCAAAAATTGGTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGAAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTAGACGTATACGCAG  >  NZ_CP009273/634348‑634611

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `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

GAAACGCATTAGCCGAATCGGCAAAAATTGGTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGAAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTAGACGTATACGCAGTATCTACCGAT  >  NZ_CP009273/634332‑634622

GAAACGCATTAGCCGAATCGGCAAAAATTGGTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAG                                                                                                                                              <  SRR3722139.82128/151‑1 (MQ=60)

     GCATTAGCCGAATCGGCAAAAATTGGTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACC                                                                                                                                         >  SRR3722139.464450/1‑151 (MQ=60)

                   GGCAAAAATTGGTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAG                                                                                                                           <  SRR3722139.453874/151‑1 (MQ=60)

                   GGCAAAAATTGGTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGG                                                                                                                             >  SRR3722139.439570/1‑149 (MQ=60)

                       agtacggtctcgtgggctcggagatgtgtataagagacagGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCG                                                                                                                         <  SRR3722139.523013/109‑1 (MQ=60)

                                 ACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTC                                                                                                              <  SRR3722139.46039/150‑1 (MQ=60)

                                     TACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACC                                                                                                          <  SRR3722139.18087/150‑1 (MQ=60)

                                               CGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTT                                                                                               <  SRR3722139.416331/151‑1 (MQ=60)

                                                        GGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTA                                                                                      <  SRR3722139.255681/151‑1 (MQ=60)

                                                            GAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCC                                                                                  >  SRR3722139.335803/1‑151 (MQ=60)

                                                                       GTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTG                                                                       >  SRR3722139.582273/1‑151 (MQ=60)

                                                                             GATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGAC                                                                 >  SRR3722139.70456/1‑151 (MQ=60)

                                                                                                   TTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGA                                             <  SRR3722139.276930/149‑1 (MQ=60)

                                                                                                        AAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAG                                      <  SRR3722139.4430/151‑1 (MQ=60)

                                                                                                               GCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGG                               >  SRR3722139.559601/1‑151 (MQ=60)

                                                                                                                  TTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCG                            >  SRR3722139.339493/1‑151 (MQ=60)

                                                                                                                               AATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTAGACGTATACGC               <  SRR3722139.480564/151‑1 (MQ=60)

                                                                                                                                    ATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTAGACGTATACGCAGTAT          >  SRR3722139.43480/1‑151 (MQ=60)

                                                                                                                                            CACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTAGACGTATACGCAGTATCTACCGAT  <  SRR3722139.437402/151‑1 (MQ=60)

GAAACGCATTAGCCGAATCGGCAAAAATTGGTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGAAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTAGACGTATACGCAGTATCTACCGAT  >  NZ_CP009273/634332‑634622

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`