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
A35 F60 I1 R1	16	64.9	2210988	99.0%	2188878	138.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,815,883	+C	coding (667/687 nt)	rph ←	truncated RNase PH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,815,879	1	.	C	92.9%	140.8 / 3.6	42	coding (671/687 nt)	rph	truncated RNase PH
Reads supporting (aligned to +/- strand): ref base . (3/0); new base C (13/26); total (16/26)
Fisher's exact test for biased strand distribution p-value = 4.88e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.68e-01

CAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATT‑C‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTC  >  NC_000913/3815741‑3816012

cAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑Ggattcgatt‑c                                                                                                                                         <  1:688370/140‑1 (MQ=255)

          gcgcTGATATGGTTTCATGCCTTCGCTCCTCCTCTTACTTTTCTACAGTCAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGc                                                                                                                             <  2:315690/140‑1 (MQ=255)

          gcgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGc                                                                                                                             <  2:569168/140‑1 (MQ=255)

                 tatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTGCAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGcc                                                                                                                      <  2:921715/140‑1 (MQ=255)

                 tatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGcc                                                                                                                      <  1:894510/140‑1 (MQ=255)

                 tatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGACCAGAGcc                                                                                                                      <  1:708453/140‑1 (MQ=255)

                  caggTTTCTTGCCTTCCCTCCTTATCTTACTTTACCACATACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCca                                                                                                                     <  2:517644/138‑1 (MQ=255)

                        tCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGa                                                                                                               >  1:575360/1‑140 (MQ=255)

                          aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATg                                                                                                             >  1:847351/1‑140 (MQ=255)

                          aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATg                                                                                                             >  2:925789/1‑140 (MQ=255)

                          aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAG‑GGATTCGATT‑CTCC‑A‑TCGGGCAAGAGCCAACAAGATg                                                                                                             >  1:295753/1‑140 (MQ=255)

                              cTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                        <  1:560405/140‑1 (MQ=255)

                               ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                        <  2:847351/140‑1 (MQ=255)

                               ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                        <  1:911507/140‑1 (MQ=255)

                                tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTGGATT‑C‑CCGC‑TCAGGACAGAGCTAACAAGATGAGtctg                                                                                                       >  1:517644/1‑137 (MQ=255)

                                 cGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCcaac                                                                                                                   <  1:60198/127‑1 (MQ=255)

                                 cGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCcaac                                                                                                                   >  2:60198/1‑127 (MQ=255)

                                           cTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTAGATT‑C‑CC‑CTTCGAGCCTGAGCCAACGAGATGAGTAGCTCTTCATgggg                                                                                            >  2:348930/1‑139 (MQ=255)

                                                     tACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTg                                                                                           <  2:224425/131‑1 (MQ=255)

                                                     tACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTg                                                                                           >  1:224425/1‑131 (MQ=255)

                                                       cAGACAAAAAAAAGGCGACTCATCAGTCGCGTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGcc                                                                                <  2:863221/140‑1 (MQ=255)

                                                        aGACAAAAAAATGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCt                                                                               >  1:1034060/1‑140 (MQ=255)

                                                              aaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGcc                                                                         <  2:1036631/140‑1 (MQ=255)

                                                              aaaaaaGGCGACTCACCAGTCGTCTCAAATATCAGTTAGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGcc                                                                         <  1:348930/140‑1 (MQ=255)

                                                                 aaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTc                                                                      <  1:617269/140‑1 (MQ=255)

                                                                    ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTCCTGCCGTcccc                                                                   >  1:1010337/1‑140 (MQ=255)

                                                                      cGACTCATGAGTCGCCATAAAAATCAGTTTGTCTGAGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                 <  2:500495/140‑1 (MQ=255)

                                                                      cGACTCATCAGTCGCTTTAAAAATCGGTTCGCCAGCGGCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                 <  1:356052/140‑1 (MQ=255)

                                                                      cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                 <  2:992120/140‑1 (MQ=255)

                                                                                   gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCaa                                                         <  2:706600/136‑1 (MQ=255)

                                                                                   gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCaa                                                         >  1:1011543/1‑136 (MQ=255)

                                                                                   gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCaa                                                         <  2:1011543/136‑1 (MQ=255)

                                                                                   gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCaa                                                         >  1:706600/1‑136 (MQ=255)

                                                                                      ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcgc                                                 >  1:812590/1‑140 (MQ=255)

                                                                                        aaaaaTCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCTCTGCACTTCAATGATGCGccc                                               <  1:562116/140‑1 (MQ=255)

                                                                                              caatttGCCAGCGCCGCCTTCTGCGTCGCTACAAG‑GTATTCGATTCC‑CC‑C‑TCGGGCCACAGCCAACAAGATGAGTAGCTCTGCATGGGTGAACGGCTCGCCTTCTGCCGCCCCCTGCACTTCAGTGATGCGCCCGTCTTc                                         <  2:1034060/137‑1 (MQ=255)

                                                                                                gTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCgg                                       <  2:575360/140‑1 (MQ=255)

                                                                                                 tttGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGt                                      <  1:839010/140‑1 (MQ=255)

                                                                                                   tGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGGTGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtca                                    <  1:1033337/140‑1 (MQ=255)

                                                                                                        gcgcCGCCTTCTGCGTCGCTACCAT‑GGATCCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACt                               <  1:370098/140‑1 (MQ=255)

                                                                                                            cgccTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGt                           <  2:571621/140‑1 (MQ=255)

                                                                                                              ccTTCTGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTc                         >  2:13575/1‑140 (MQ=255)

                                                                                                                   tGCGTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTc                    >  1:60980/1‑140 (MQ=255)

                                                                                                                      gTCGCTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt                 <  2:812590/140‑1 (MQ=255)

                                                                                                                          cTACAAT‑GGATTCGATTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTctct             >  1:638955/1‑140 (MQ=255)

                                                                                                                                      tcgattcC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTc  >  1:21358/1‑140 (MQ=255)

                                                                                                                                      tcgattcC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTc  >  1:143803/1‑140 (MQ=255)

CAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAT‑GGATTCGATT‑C‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTC  >  NC_000913/3815741‑3816012

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A