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	1,060,660	T→C	L390P (CTC→CCC)	yccE →	YccE family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,060,660	0	T	C	100.0%	71.5 / NA	20	L390P (CTC→CCC)	yccE	YccE family protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (12/8); total (12/8)

TAGCATTTGCTCATTATTTATTGTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCTCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTAAAAACCATTGTTAT  >  NZ_CP009273/1060529‑1060780

tAGCATTTGCTCATTATTTATTGTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCcctcct                                                                                                                   >  2:165905/1‑139 (MQ=255)

             ttatttatTGTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCt                                                                                                       >  1:460181/1‑138 (MQ=255)

                      gTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTAc                                                                                              >  1:161321/1‑138 (MQ=255)

                                 tgtgGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACaa                                                                                   >  1:452928/1‑138 (MQ=255)

                                                      gaatgaatCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTc                                                             <  2:161321/139‑1 (MQ=255)

                                                         tgaatCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGAc                                                          >  1:359158/1‑139 (MQ=255)

                                                                                    tGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCt                                                                                                       <  1:347386/67‑1 (MQ=255)

                                                                                    tGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCt                                                                                                       >  2:347386/1‑67 (MQ=255)

                                                                                     gAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTaa                                  <  2:484242/135‑1 (MQ=255)

                                                                                                       aaCACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTaaaaa            >  2:586326/1‑139 (MQ=255)

                                                                                                                 aTCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTAAAAACCATTGttat  >  2:251953/1‑139 (MQ=255)

                                                                                                                 aTCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTAAAAACCATTGttat  <  1:165905/139‑1 (MQ=255)

                                                                                                                      tATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATgcg                                                                   <  1:544845/69‑1 (MQ=255)

                                                                                                                      tATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATgcg                                                                   >  2:544845/1‑69 (MQ=255)

                                                                                                                             tttACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGa                                                           >  1:526793/1‑70 (MQ=255)

                                                                                                                             tttACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGa                                                           <  2:526793/70‑1 (MQ=255)

                                                                                                                               tACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAaatgaatg                                                                     >  1:47716/1‑58 (MQ=255)

                                                                                                                               tACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAaatgaatg                                                                     <  2:47716/58‑1 (MQ=255)

                                                                                                                               tACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTaaa                                                  >  2:416206/1‑77 (MQ=255)

                                                                                                                               tACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTaaa                                                  <  1:416206/77‑1 (MQ=255)

TAGCATTTGCTCATTATTTATTGTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCTCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTAAAAACCATTGTTAT  >  NZ_CP009273/1060529‑1060780

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 18 ≤` `ATCG/ATCG` `< 35 ≤` `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

TTCTTGTTGTTCTTTCAGATAGCATTTGCTCATTATTTATTGTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCTCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTAAAAACCATTGTTATTAGTCTCACACTTT  >  NZ_CP009273/1060510‑1060794

TTCTTGTTGTTCTTTCAGATAGCATTTGCTCATTATTTATTGTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCC                                                                                                                                        >  SRR3722135.490742/1‑151 (MQ=60)

                     GCATTTGCTCATTATTTATTGTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTC                                                                                                                    >  SRR3722135.466430/1‑150 (MQ=60)

                              cagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAA                                                                                                          <  SRR3722135.352301/89‑1 (MQ=60)

                              CATTATTTATTGTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACA                                                                                                           >  SRR3722135.163540/1‑150 (MQ=60)

                                         GTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAAT                                                                                                >  SRR3722135.459056/1‑150 (MQ=60)

                                                                 TCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACT                                                                       >  SRR3722135.364234/1‑151 (MQ=60)

                                                                  gaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagCTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTA                                                                      <  SRR3722135.552054/91‑1 (MQ=60)

                                                                                   catacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAA                                                     <  SRR3722135.421926/99‑1 (MQ=60)

                                                                                                                                   AATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTAAAAACCATTGTTATTAGTCTCACAC     <  SRR3722135.168213/151‑1 (MQ=60)

                                                                                                                                     TCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtctt   >  SRR3722135.533769/1‑92 (MQ=60)

                                                                                                                                       ATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctgcttgaaaa  >  SRR3722135.48344/1‑80 (MQ=60)

TTCTTGTTGTTCTTTCAGATAGCATTTGCTCATTATTTATTGTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCTCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTAAAAACCATTGTTATTAGTCTCACACTTT  >  NZ_CP009273/1060510‑1060794

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: `‑`