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 F4 I96 R1	227	23.3	882352	98.0%	864704	126.9

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	100.0%	100.5 / NA	29	E26G (GAA→GGA)	ahpC	alkyl hydroperoxide reductase subunit C
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (16/13); total (16/13)

AATCGGCAAAAATTGGTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGAAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTAGACGTATACGCA  >  NZ_CP009273/634347‑634610

aaTCGGCAAAAATTGGTTACCTTACTTCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATa                                                                                                                               >  2:413091/1‑139 (MQ=255)

aaTCGGCAAAAATTGGTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATa                                                                                                                               >  1:72241/1‑139 (MQ=255)

aaTCGGCAAAAATTGGTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATa                                                                                                                               >  1:18458/1‑139 (MQ=255)

               gTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGa                                                                                                                <  1:94529/139‑1 (MQ=255)

                             cATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGtcttcttcttc                                                                                                  >  2:112248/1‑139 (MQ=255)

                              aTCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGtcttcttcttc                                                                                                  >  1:370464/1‑138 (MQ=255)

                              aTCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGtcttcttcttc                                                                                                  >  1:16503/1‑138 (MQ=255)

                              aTCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGtcttc                                                                                                        <  1:197777/132‑1 (MQ=255)

                              aTCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGtcttc                                                                                                        >  2:197777/1‑132 (MQ=255)

                                            ggaAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGactt                                                                                    >  2:172380/1‑138 (MQ=255)

                                                        gTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGc                                                                       >  2:134886/1‑139 (MQ=255)

                                                          ccTTGTTTAACACCAAAATTAAACTTTTTAAAAACCAGGCTTTCAAAAACGGCAAATTAATCGAAATAACCGGAAAAGAAACCGAAGCCCCCTGGAGCGCCTTTTTCTTCAACCGGCCTGACTTTACTTTCGAATGccg                                                                     >  2:32862/1‑138 (MQ=255)

                                                           cTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGccc                                                                     >  2:145249/1‑138 (MQ=255)

                                                                ttAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCccgaccga                                                               <  1:244978/139‑1 (MQ=255)

                                                                    cacCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTg                                                           >  1:311036/1‑139 (MQ=255)

                                                                    cacCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTg                                                           >  2:36836/1‑139 (MQ=255)

                                                                         aaaTTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGa                                                      >  1:8963/1‑139 (MQ=255)

                                                                           aTTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACg                                                    <  2:87473/139‑1 (MQ=255)

                                                                               aaCCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTg                                                 <  1:36836/138‑1 (MQ=255)

                                                                                     ttAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGAc                                            <  1:127407/137‑1 (MQ=255)

                                                                                             cAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACgaag                                  <  2:347046/139‑1 (MQ=255)

                                                                                                        aaaCGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGaaa                       <  1:172380/139‑1 (MQ=255)

                                                                                                              cGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGc                 >  2:128566/1‑139 (MQ=255)

                                                                                                              cGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGc                 >  1:29592/1‑139 (MQ=255)

                                                                                                                          aaTCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTAGACGTATAc     <  1:32862/139‑1 (MQ=255)

                                                                                                                           aTCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTAGACGTATACg    <  2:29592/139‑1 (MQ=255)

                                                                                                                           aTCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTAGACGTATACg    <  1:128566/139‑1 (MQ=255)

                                                                                                                           aTCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTAGACGTATACg    <  1:112248/139‑1 (MQ=255)

                                                                                                                              aCCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTAGACGTATACGCa  <  1:329724/138‑1 (MQ=255)

AATCGGCAAAAATTGGTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGAAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTAGACGTATACGCA  >  NZ_CP009273/634347‑634610

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `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

GAAACGCATTAGCCGAATCGGCAAAAATTGGTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGAAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTAGACGTATACGCAGTATCTACCGA  >  NZ_CP009273/634332‑634621

gcagaagacggcatacgagattcgccttagtctcgtgggctcggagatgtgtataagagacagGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAG                                                                                                                                             <  SRR3722119.187405/88‑1 (MQ=60)

    CGCATTAGCCGAATCGGCAAAAATTGGTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATAC                                                                                                                                         >  SRR3722119.72939/1‑151 (MQ=60)

    CGCATTAGCCGAATCGGCAAAAATTGGTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATAC                                                                                                                                         >  SRR3722119.18633/1‑151 (MQ=60)

                             GGTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTC                                                                                                                <  SRR3722119.95453/151‑1 (MQ=60)

                                  CCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCT                                                                                                            >  SRR3722119.16645/1‑150 (MQ=60)

                                  CCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCT                                                                                                            >  SRR3722119.374201/1‑150 (MQ=60)

                                      ACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCC                                                                                                        <  SRR3722119.199887/150‑1 (MQ=60)

                                                                        TCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGG                                                                     >  SRR3722119.314206/1‑151 (MQ=60)

                                                                             GATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGAC                                                                >  SRR3722119.9033/1‑151 (MQ=60)

                                                                              ATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACG                                                               <  SRR3722119.247526/151‑1 (MQ=60)

                                                                                             AAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTAC                                                 <  SRR3722119.37160/150‑1 (MQ=60)

                                                                                                   TTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGA                                            <  SRR3722119.128676/149‑1 (MQ=60)

                                                                                                                  TTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCG                           >  SRR3722119.29854/1‑151 (MQ=60)

                                                                                                                      AAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTAGA                       <  SRR3722119.174154/151‑1 (MQ=60)

                                                                                                                                        AAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTAGACGTATACGCAGTATCTAC     <  SRR3722119.33144/151‑1 (MQ=60)

                                                                                                                                         AATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTAGACGTATACGCAGTATCTACC    <  SRR3722119.129847/151‑1 (MQ=60)

                                                                                                                                         AATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTAGACGTATACGCAGTATCTACC    <  SRR3722119.113347/151‑1 (MQ=60)

                                                                                                                                            CACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTAGACGTATACGCAGTATCTACCGA  <  SRR3722119.333078/150‑1 (MQ=60)

GAAACGCATTAGCCGAATCGGCAAAAATTGGTTACCTTACATCTCATCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGAAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGAAGAACTGCAGAAACTGGGCGTAGACGTATACGCAGTATCTACCGA  >  NZ_CP009273/634332‑634621

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`