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
A0 F0 I1 R1	715	38.4	1606192	96.6%	1551581	120.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,796,916	T→C	Y38C (TAT→TGT)	yqaE ←	cyaR sRNA‑regulated protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,796,916	0	T	C	97.6%	147.8 / NA	42	Y38C (TAT→TGT)	yqaE	cyaR sRNA‑regulated protein
Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (14/27); minor base A (1/0); total (15/27)
Fisher's exact test for biased strand distribution p-value = 3.57e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

CTACCTCATTCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATATACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAACCCATATGTACTCCCTATAAGAAAAT  >  NC_000913/2796789‑2797049

cTACCTCATTCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAgt                                                                                                                            <  2:775675/139‑1 (MQ=255)

  aCCTCATTCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAgtgt                                                                                                                          <  1:137411/139‑1 (MQ=255)

  aCCTCATTCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAgtgt                                                                                                                          >  2:597433/1‑139 (MQ=255)

    cTCATTCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCa                                                                                                                        >  2:301469/1‑139 (MQ=255)

      cATTCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGTGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAAc                                                                                                                      <  2:477725/139‑1 (MQ=255)

      cATTCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAAc                                                                                                                      <  1:728470/139‑1 (MQ=255)

        ttCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAg                                                                                                                    >  1:525871/1‑139 (MQ=255)

        ttCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAg                                                                                                                    <  2:274263/139‑1 (MQ=255)

        ttCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAg                                                                                                                    <  1:597433/139‑1 (MQ=255)

             tAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAatat                                                                                                               <  1:742792/139‑1 (MQ=255)

                          cAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGc                                                                                                  >  1:492046/1‑139 (MQ=255)

                             aaaGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCa                                                                                               >  1:651296/1‑139 (MQ=255)

                                 tgtAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAgtgt                                                                                                                          >  1:198234/1‑108 (MQ=255)

                                 tgtAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAgtgt                                                                                                                          <  2:198234/108‑1 (MQ=255)

                                 tgtAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCg                                                                                           <  2:34210/139‑1 (MQ=255)

                                  gtAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGa                                                                                          <  2:451898/139‑1 (MQ=255)

                                   tAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGCGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCATGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGaa                                                                                         >  2:535292/1‑139 (MQ=255)

                                   tAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAATGCCCAACCGaa                                                                                         >  1:726721/1‑139 (MQ=255)

                                        gagGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCtt                                                                                    <  1:535292/139‑1 (MQ=255)

                                           gAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAg                                                                                                                                >  2:103666/1‑92 (MQ=255)

                                           gAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAg                                                                                                                                <  1:103666/92‑1 (MQ=255)

                                                cggcgCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGagc                                                                            >  2:580609/1‑139 (MQ=255)

                                                 ggcgCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTCTGCACCCAGAACGCGTGAATCAAACCGGGGATGCACCGAAGCAGTTTCAACAGAATAATAAGAATGAACGCCCAACCGAACCCTTTACCGagca                                                                           <  1:631922/139‑1 (MQ=255)

                                                              cgcgGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAgcgg                                                              <  1:301469/139‑1 (MQ=255)

                                                                 ggggATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGcggcgg                                                           <  2:697416/139‑1 (MQ=255)

                                                                     aTGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGa                                                       <  2:651296/139‑1 (MQ=255)

                                                                      tGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGaa                                                      <  1:327589/139‑1 (MQ=255)

                                                                        aGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAatg                                                    >  1:154860/1‑139 (MQ=255)

                                                                           acaGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAatgatg                                                 <  1:785039/139‑1 (MQ=255)

                                                                                              tGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGa                              <  1:580609/139‑1 (MQ=255)

                                                                                              tGCACCCAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGa                              <  1:719492/139‑1 (MQ=255)

                                                                                                  cccAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAAcc                          <  1:580447/139‑1 (MQ=255)

                                                                                                   ccAGAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAAccc                         <  2:525871/139‑1 (MQ=255)

                                                                                                      gAACGCGTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAACCCata                      >  1:267304/1‑139 (MQ=255)

                                                                                                         cgcgTGAATCAATCCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTCACTGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAACCCATATGt                   <  2:678803/139‑1 (MQ=255)

                                                                                                          gcgTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAACCCATATGTa                  <  2:267304/139‑1 (MQ=255)

                                                                                                          gcgTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAACCCATATGTa                  <  2:572709/139‑1 (MQ=255)

                                                                                                          gcgTGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAACCCATATGTa                  <  2:154860/139‑1 (MQ=255)

                                                                                                             tGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAACCCatat                     >  1:183059/1‑133 (MQ=255)

                                                                                                             tGAATCAAACCGGGGATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAACCCatat                     <  2:183059/133‑1 (MQ=255)

                                                                                                                     aCCGGGGATAAACCCAAGTAGTGTCAACAGAATATTAATAATGAACGCGCAACCGAACGCCTTACCGAGCAGAACGCCGAGCGGCGGTAAAAGGATGGTGACGACGATTCTCCCGAAATCTATAAGTACTCCCTATaac       >  1:191717/1‑138 (MQ=255)

                                                                                                                          ggATACACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAACCCATATGTACTCCCTATAAGAAAAt  >  2:105630/1‑139 (MQ=255)

CTACCTCATTCGTTAACGGAAACACTCAGAAAGTGTAGCAGAGGAACGCGGCGCGTTAACGCCGCGGGGATGAGCACAGGTTTAATCGCGGGTTTGCACCCAGAACGCGTGAATCAAACCGGGGATATACCCAAGCAGTGTCAACAGAATATTAATAATGAACGCCCAACCGAACCCTTTACCGAGCAGCACGCCGAGCGGCGGCAGAATGATGGTGATGACGATTCTCCAGAAACCCATATGTACTCCCTATAAGAAAAT  >  NC_000913/2796789‑2797049

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A